IMT Institutional Repository: No conditions. Results ordered -Date Deposited. 2024-03-29T00:47:26ZEPrintshttp://eprints.imtlucca.it/images/logowhite.pnghttp://eprints.imtlucca.it/2017-11-13T15:58:37Z2017-11-13T15:58:37Zhttp://eprints.imtlucca.it/id/eprint/3827This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/38272017-11-13T15:58:37ZOn Economic Complexity and the Fitness of NationsComplex economic systems can often be described by a network, with nodes representing economic entities and edges their interdependencies, while network centrality is often a good indicator of importance. Recent publications have implemented a nonlinear iterative Fitness-Complexity (FC) algorithm to measure centrality in a bipartite trade network, which aims to represent the ‘Fitness’ of national economies as well as the ‘Complexity’ of the products being traded. In this paper, we discuss this methodological approach and conclude that further work is needed to identify stable and reliable measures of fitness and complexity. We provide theoretical and numerical evidence for the intrinsic instability in the nonlinear definition of the FC algorithm. We perform an in-depth evaluation of the algorithm’s rankings in two real world networks at the country level: the global trade network, and the patent network in different technological domains. In both networks, we find evidence of the instabilities predicted theoretically, and show that ‘complex’ products or patents tend often to be those that countries rarely produce, rather than those that are intrinsically more difficult to produce.Greg MorrisonSergey V. BuldyrevMichele ImbrunoOmar Alonso Doria ArrietaArmando Rungiarmando.rungi@imtlucca.itMassimo Riccabonimassimo.riccaboni@imtlucca.itFabio Pammolli2017-09-04T09:15:17Z2017-09-04T09:20:20Zhttp://eprints.imtlucca.it/id/eprint/3767This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/37672017-09-04T09:15:17ZGlobal ownership and corporate control networksIn this contribution, at first, we introduce a basic network framework to study pyramidal structures and wedges between ownership and control of companies. Then, we apply it to a dataset of
53.5 million of companies operating in 208 countries. Among others, we detect a strong concentra-
tion of corporate power, as less than 1% of parent companies collect more than 100 subsidiaries, but
they are responsible for more than 50% of global sales. Therefore, we show that the role of indirect
control, i.e., through middlemen subsidiaries, is relevant in 15% of domestic and 54% of foreign
subsidiaries. Among foreign companies, cases emerge of blurring nationality, when control paths
cross more than one national border, in the presence of multiple passports (19.1%), indirectly for-
eign (24.5%), and round-tripping subsidiaries (1.33%). Finally, we relate indirect control strategies
to country indicators of the institutional environment. We find that pyramidal structures arise less
likely in the presence of good financial and contractual institutions in the parent's country, as these
foster more transparent forms of corporate governance. Instead, parent companies choose indirect
control through countries of subsidiaries that have better financial institutions, possibly because it
is easier to coordinate decisions from remote. Finally, we find that offshore financial centers are
preferred jurisdictions for middlemen subsidiaries, probably due to a lower taxation and a lack of
financial disclosure.Armando Rungiarmando.rungi@imtlucca.itGreg MorrisonFabio Pammolli2017-05-08T12:56:40Z2018-01-31T12:42:32Zhttp://eprints.imtlucca.it/id/eprint/3700This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/37002017-05-08T12:56:40ZModeling networks with a growing feature-structureWe present a new network model accounting for multidimensional assortativity. Each node is characterized by a number of features and the probability of a link between two nodes depends on common features. We do not fix a priori the total number of possible features. The bipartite network of the nodes and the features evolves according to a stochastic dynamics that depends on
three parameters that respectively regulate the preferential attachment in the transmission of the features to the nodes, the number of new features per node, and the power-law behavior of the total number of observed features.
Our model also takes into account a mechanism of triadic closure. We provide theoretical results and statistical estimators for the parameters of the model.
We validate our approach by means of simulations and an empirical analysis of a network of scientific collaborations.Irene Crimaldiirene.crimaldi@imtlucca.itMichela Del Vicariomichela.delvicario@imtlucca.itGreg Morrisongreg.morrison@imtlucca.itWalter Quattrociocchiwalter.quattrociocchi@imtlucca.itMassimo Riccabonimassimo.riccaboni@imtlucca.it2015-11-03T10:10:07Z2015-11-03T10:10:07Zhttp://eprints.imtlucca.it/id/eprint/2805This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/28052015-11-03T10:10:07ZGeneralized Erdos Numbers for network analysisIn this paper we consider the concept of `closeness' between nodes in a weighted network that can be defined topologically even in the absence of a metric. The Generalized Erd\H{o}s Numbers (GENs) satisfy a number of desirable properties as a measure of topological closeness when nodes share a finite resource between nodes as they are real-valued and non-local, and can be used to create an asymmetric matrix of connectivities. We show that they can be used to define a personalized measure of the importance of nodes in a network with a natural interpretation that leads to a new global measure of centrality and is highly correlated with Page Rank. The relative asymmetry of the GENs (due to their non-metric definition) is linked also to the asymmetry in the mean first passage time between nodes in a random walk, and we use a linearized form of the GENs to develop a continuum model for `closeness' in spatial networks. As an example of their practicality, we deploy them to characterize the structure of static networks and show how it relates to dynamics on networks in such situations as the spread of an epidemic.Greg Morrisongreg.morrison@imtlucca.itLevi DudteL. Mahadevan2015-09-30T07:39:33Z2015-09-30T07:39:33Zhttp://eprints.imtlucca.it/id/eprint/2753This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/27532015-09-30T07:39:33ZThe Similarity of Global Value Chains: a Network-Based MeasureInternational trade has been increasingly organized in the form of global value chains
(GVCs) where different stages of production are located in dfferent countries. This
recent phenomenon has substantial consequences for both trade policy design at the
national or regional level and business decision making at the form level. In this paper,
we provide a new method for comparing GVCs across countries and over time. First,
we use the World Input-Output Database (WIOD) to construct both the upstream and
downstream global value networks, where the nodes are individual sectors in dfferent
countries and the links are the value-added contribution relationships. Second, we introduce
a network-based measure of node similarity to compare the GVCs between any
pair of countries for each sector and each year available in the WIOD. Our networkbased
similarity is a better measure for node comparison than the existing ones because
it takes into account all the direct and indirect relationships between country-sector
pairs, is applicable to both directed and weighted networks with self-loops, and takes
into account externally defined node attributes. As a result, our measure of similarity
reveals the most intensive interactions among the GVCs across countries and over time.
From 1995 to 2011, the average similarity between sectors and countries have clear increasing
trends, which are temporarily interrupted by the recent economic crisis. This
measure of the similarity of GVCs provides quantitative answers to important questions
about dependency, sustainability, risk, and competition in the global production
system.Zhen Zhuzhen.zhu@imtlucca.itGreg Morrisongreg.morrison@imtlucca.itMichelangelo Puligamichelangelo.puliga@imtlucca.itAlessandro Chessaalessandro.chessa@imtlucca.itMassimo Riccabonimassimo.riccaboni@imtlucca.it2015-05-05T12:20:47Z2017-05-09T09:27:37Zhttp://eprints.imtlucca.it/id/eprint/2667This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/26672015-05-05T12:20:47ZHomophily and Triadic Closure in Evolving Social NetworksWe present a new network model accounting for homophily and triadic closure in the evolution of social networks. In particular, in our model, each node is characterized by a number of features and the probability of a link between
two nodes depends on common features. The bipartite network of the actors and features evolves according to a dynamics that depends on three parameters that respectively regulate the preferential attachment in the transmission
of the features to the nodes, the number of new features per node, and the power-law behavior of the total number of observed features. We provide theoretical results and statistical estimators for the parameters of the model.
We validate our approach by means of simulations and an empirical analysis of a network of scientifc collaborations.Irene Crimaldiirene.crimaldi@imtlucca.itMichela Del Vicariomichela.delvicario@imtlucca.itGreg Morrisongreg.morrison@imtlucca.itWalter Quattrociocchiwalter.quattrociocchi@imtlucca.itMassimo Riccabonimassimo.riccaboni@imtlucca.it2014-09-02T10:30:20Z2015-04-21T08:20:39Zhttp://eprints.imtlucca.it/id/eprint/2274This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/22742014-09-02T10:30:20ZBorder sensitive centrality in global patent citation networksWhen resources are shared between interacting networks, the importance of each node depends strongly on how collaborative or competitive each sub-network is. In this paper, we develop a new method of measuring centrality in the complex network of patent citations that can take political borders into account, where the national benefit of domestic citations relative to foreign citations can be controlled by a free parameter. We find that while some patent classes are of high importance both in the global and the domestic economy, there often exist patent classes in individual countries that are more central nationally than in global economy. We characterize the most important classes globally and domestically for six different nations, and describe their robustness to various perturbations to the model and to noise. Greg Morrisongreg.morrison@imtlucca.itEleftherios GiovanisFabio Pammollif.pammolli@imtlucca.itMassimo Riccabonimassimo.riccaboni@imtlucca.it2014-02-04T10:17:30Z2014-03-05T12:05:36Zhttp://eprints.imtlucca.it/id/eprint/2130This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/21302014-02-04T10:17:30ZBorder sensitive centralities in patent citation networks using asymmetric random walksGrowth and innovation in particular sectors of the economy can be spurred by funding from governments or firms with the initial investment producing spillovers into other sectors of the economy. Funding sectors that are central to the economy are expected to produce more or greater spillovers than if more peripheral sectors were funded. If the funding body is a national government, it is desirable that spillovers remain primarily in the domestic economy rather than targeting globally central sectors and risk subsidizing a foreign economy. In this paper, we develop a new method of measuring centrality in the complex network of patent citations that can take national borders into account, where the importance of domestic citations relative to foreign citations can be controlled by a free parameter. We find empirically that while some patent classes are of high importance both in the global and the domestic economy, there often exist patent classes in individual countries that are more central nationally than in global economy.Greg Morrisongreg.morrison@imtlucca.itEleftherios Giovaniseleftherios.giovanis@imtlucca.itFabio Pammollif.pammolli@imtlucca.itMassimo Riccabonimassimo.riccaboni@imtlucca.it2013-10-04T11:04:59Z2013-10-04T11:04:59Zhttp://eprints.imtlucca.it/id/eprint/1829This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18292013-10-04T11:04:59ZDiscovering Communities through FriendshipWe introduce a new method for detecting communities of arbitrary size in an undirected weighted network. Our approach is based on tracing the path of closest‐friendship between nodes in the network using the recently proposed Generalized Erds Numbers. This method does not require the choice of any arbitrary parameters or null models, and does not suffer from a system‐size resolution limit. Our closest‐friend community detection is able to accurately reconstruct the true network structure for a large number of real world and artificial benchmarks, and can be adapted to study the multi‐level structure of hierarchical communities as well. We also use the closeness between nodes to develop a degree of robustness for each node, which can assess how robustly that node is assigned to its community. To test the efficacy of these methods, we deploy them on a variety of well known benchmarks, a hierarchal structured artificial benchmark with a known community and robustness structure, as well as real‐world networks of coauthorships between the faculty at a major university and the network of citations of articles published in Physical Review. In all cases, microcommunities, hierarchy of the communities, and variable node robustness are all observed, providing insights into the structure of the network.Greg Morrisongreg.morrison@imtlucca.itL. Mahadevan2013-10-04T10:56:22Z2013-10-04T11:09:42Zhttp://eprints.imtlucca.it/id/eprint/1828This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18282013-10-04T10:56:22ZNew Encoding Schemes with InfofusesKyeng Min ParkChoongik KimSamuel W. Thomas IIIHyo Jae YoonGreg Morrisongreg.morrison@imtlucca.itL. MahadevanGeorge M. Whitesides2013-10-04T10:35:35Z2013-10-04T11:05:22Zhttp://eprints.imtlucca.it/id/eprint/1826This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18262013-10-04T10:35:35ZRobust error correction in infofusesAn infofuse is a combustible fuse in which information is encoded through the patterning of metallic salts, with transmission in the optical range simply associated with burning. The constraints, advantages and unique error statistics of physical chemistry require us to rethink coding and decoding schemes for these systems. We take advantage of the non-binary nature of our signal with a single bit representing one of N=7 states to produce a code that, using a single or pair of intensity thresholds, allows the recovery of the intended signal with an arbitrarily high recovery probability, given reasonable assumptions about the distribution of errors in the system. An analysis of our experiments with infofuses shows that the code presented is consistent with these schemes, and encouraging for the field of chemical communication and infochemistry given the vast permutations and combinations of allowable non-binary signals. Greg Morrisongreg.morrison@imtlucca.itSamuel W. Thomas IIIChristopher N. LaFrattaJian GuoManuel A. PalaciosSameer SonkusaleDavid R. WaltGeorge M. WhitesidesL. Mahadevan2013-10-04T10:29:32Z2014-12-05T09:20:01Zhttp://eprints.imtlucca.it/id/eprint/1825This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18252013-10-04T10:29:32ZCompaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experimentsWe establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (Pfold=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that Pfold is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.Greg Morrisongreg.morrison@imtlucca.itChangbong HyeonMichael HinczewskiD. Thirumalai2013-10-04T10:20:55Z2013-10-04T10:20:55Zhttp://eprints.imtlucca.it/id/eprint/1824This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18242013-10-04T10:20:55ZAsymmetric network connectivity using weighted harmonic averagesWe propose a non-metric measure of the "closeness" felt between two nodes in an undirected, weighted graph using a simple weighted harmonic average of connectivity, that is a real-valued Generalized Erdös Number (GEN). While our measure is developed with a collaborative network in mind, the approach can be of use in a variety of artificial and real-world networks. We are able to distinguish between network topologies that standard distance metrics view as identical, and use our measure to study some simple analytically tractable networks. We show how this might be used to look at asymmetry in authorship networks such as those that inspired the integer Erdös numbers in mathematical coauthorships. We also show the utility of our approach to devise a ratings scheme that we apply to the data from the NetFlix prize, and find a significant improvement using our method over a baseline.Greg Morrisongreg.morrison@imtlucca.itL. Mahadevan2013-10-04T10:11:06Z2013-11-21T12:19:48Zhttp://eprints.imtlucca.it/id/eprint/1823This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18232013-10-04T10:11:06ZTheoretical Perspectives on Protein FoldingUnderstanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and timescales of folding are, to a large extent, determined by N, the number of residues. The intricate details of folding as a function of denaturant concentration can be predicted by using a novel coarse-grained molecular transfer model. By watching one molecule fold at a time, using single-molecule methods, investigators have established the validity of the theoretically anticipated heterogeneity in the folding routes and the N-dependent timescales for the three stages in the approach to the native state. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the protein folding problem in the broadest sense.D. ThirumalaiEdward P. O'BrienGreg Morrisongreg.morrison@imtlucca.itChangbong Hyeon2013-10-04T10:07:03Z2013-10-04T10:07:03Zhttp://eprints.imtlucca.it/id/eprint/1822This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18222013-10-04T10:07:03ZHow accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?Single molecule Förster resonance energy transfer (FRET) experiments are used to infer the properties of the denatured state ensemble (DSE) of proteins. From the measured average FRET efficiency, 〈E〉, the distance distribution P(R) is inferred by assuming that the DSE can be described as a polymer. The single parameter in the appropriate polymer model (Gaussian chain, wormlike chain, or self-avoiding walk) for P(R) is determined by equating the calculated and measured 〈E〉. In order to assess the accuracy of this “standard procedure,” we consider the generalized Rouse model (GRM), whose properties [〈E〉 and P(R)] can be analytically computed, and the Molecular Transfer Model for protein L for which accurate simulations can be carried out as a function of guanadinium hydrochloride (GdmCl) concentration. Using the precisely computed 〈E〉 for the GRM and protein L, we infer P(R) using the standard procedure. We find that the mean end-to-end distance can be accurately inferred (less than 10% relative error) using 〈E〉 and polymer models for P(R). However, the value extracted for the radius of gyration (Rg) and the persistence length (lp) are less accurate. For protein L, the errors in the inferred properties increase as the GdmCl concentration increases for all polymer models. The relative error in the inferred Rg and lp, with respect to the exact values, can be as large as 25% at the highest GdmCl concentration. We propose a self-consistency test, requiring measurements of 〈E〉 by attaching dyes to different residues in the protein, to assess the validity of describing DSE using the Gaussian model. Application of the self-consistency test to the GRM shows that even for this simple model, which exhibits an order→disorder transition, the Gaussian P(R) is inadequate. Analysis of experimental data of FRET efficiencies with dyes at several locations for the cold shock protein, and simulations results for protein L, for which accurate FRET efficiencies between various locations were computed, shows that at high GdmCl concentrations there are significant deviations in the DSE P(R) from the Gaussian model.Edward P. O’BrienGreg Morrisongreg.morrison@imtlucca.itBernard R. BrooksD. Thirumalai2013-10-04T10:03:20Z2014-12-18T15:39:58Zhttp://eprints.imtlucca.it/id/eprint/1821This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18212013-10-04T10:03:20ZSemiflexible chains in confined spacesWe develop an analytical method for studying the properties of a noninteracting wormlike chain (WLC) in confined geometries. The mean-field-like theory replaces the rigid constraints of confinement with average constraints, thus allowing us to develop a tractable method for treating a WLC wrapped on the surface of a sphere, and fully encapsulated within it. The efficacy of the theory is established by reproducing the exact correlation functions for a WLC confined to the surface of a sphere. In addition, the coefficients in the free energy are exactly calculated. We also describe the behavior of a surface-confined chain under external tension that is relevant for single molecule experiments on histone-DNA complexes. The force-extension curves display spatial oscillations, and the extension of the chain, whose maximum value is bounded by the sphere diameter, scales as f−1 at large forces, in contrast to the unconfined chain that approaches the contour length as f−1∕2. A WLC encapsulated in a sphere, that is relevant for the study of the viral encapsulation of DNA, can also be treated using the mean-field approach. The predictions of the theory for various correlation functions are in excellent agreement with Langevin simulations. We find that strongly confined chains are highly structured by examining the correlations using a local winding axis. The predicted pressure of the system is in excellent agreement with simulations but, as is known, is significantly lower than the pressures seen for DNA packaged in viral capsids.Greg Morrisongreg.morrison@imtlucca.itD. Thirumalai2013-10-04T09:56:41Z2013-11-21T12:19:10Zhttp://eprints.imtlucca.it/id/eprint/1820This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18202013-10-04T09:56:41ZRefolding dynamics of stretched biopolymers upon force quenchSingle-molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench by using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, τF, depends asymmetrically on δfS = f S − f m and δf Q = f m − f Q where f S (f Q) is the stretch (quench) force and f m is the transition midforce of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension, R(t), occurs in three stages: A rapid initial decrease in the extension is followed by a plateau and finally, an abrupt reduction in R(t) occurs as the native state is approached. The duration of the plateau increases as λ = τ Q/τ F decreases (where τ Q is the time in which the force is reduced from f S to f Q). Variations in the mechanisms of force-quench relaxation as λ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in R(t). The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding.Changbong HyeonGreg Morrisongreg.morrison@imtlucca.itDavid L. PincusD. Thirumalai2013-10-04T09:45:11Z2013-10-04T09:45:11Zhttp://eprints.imtlucca.it/id/eprint/1819This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18192013-10-04T09:45:11ZInfochemistry: Encoding Information as Optical Pulses Using Droplets in a Microfluidic Device This article describes a new procedure for generating and transmitting a message—a sequence of optical pulses—by aligning a mask (an opaque sheet containing transparent “windows”) below a microfluidic channel in which flows an opaque continuous fluid containing transparent droplets. The optical mask encodes the message as a unique sequence of windows that can transmit or block light; the flow of transparent droplets in the channel converts this message into a sequence of optical pulses. The properties of the windows on the mask (e.g., their size, wavelength of transmittance, orientation of polarization) determine the information carried in these optical pulses (e.g., intensity, color, polarization). The structure of a transmitted signal depends on the number and spacing of droplets in the channel. Fourier transformation can deconvolve superimposed signals created by the flow of multiple droplets into the message that a single droplet would transmit. The research described in this contribution explores a new field at the intersection of chemistry, materials science, and information technology: infochemistry. Michinao HashimotoJi FengRoger L. YorkAudrey K. EllerbeeGreg Morrisongreg.morrison@imtlucca.itSamuel W. Thomas IIIL. MahadevanGeorge M. Whitesides2013-10-04T09:27:38Z2013-10-04T09:52:49Zhttp://eprints.imtlucca.it/id/eprint/1818This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18182013-10-04T09:27:38ZKinetics of Loop Formation in Polymer ChainsWe investigate the kinetics of loop formation in ideal flexible polymer chains (the Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is τc τ0N2 (where τ0 is a microscopic time scale and N is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when a, the capture radius for contact formation, exceeds b, the average distance between two connected beads. Simulations also show that when a < b, τc Nατ, where 1.5 < ατ ≤ 2 in the range 7 < N < 200 used in the simulations. By using a diffusion coefficient that is dependent on the length scales a and b (with a < b), which captures the two-stage mechanism by which looping occurs when a < b, we obtain an analytic expression for τc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly effected when interactions between monomers are taken into account. Remarkably, for N < 100, the values of τc decrease by more than 2 orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for τc to a power law in N (τc Nατ) show that ατ varies from about 2.4 in a good solvent to about 1.0 in poor solvents. The effective exponent ατ decreases as the strength of the attractive monomer−monomer interactions increases. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain. The time for contact formation between beads that are interior to the chain in good solvents changes nonmonotonically as the loop length varies. In contrast, the variation in interior loop closure time is monotonic in poor solvents. The implications of our results for contact formation in polypeptide chains, RNA, and single-stranded DNA are briefly outlined. Ngo Minh ToanGreg Morrisongreg.morrison@imtlucca.itChangbong HyeonD. Thirumalai2013-10-04T09:15:39Z2013-11-21T12:17:44Zhttp://eprints.imtlucca.it/id/eprint/1816This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18162013-10-04T09:15:39ZForce-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapesThe sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated by using single-molecule force-clamp experiments by attaching semiflexible polymers to the ends of hairpins, have been used to infer their folding landscapes. Using simulations and theory, we study the effect of the dynamics of the attached handles on the handle-free RNA free-energy profile Foeq(zm), where zm is the molecular extension of the hairpin. Accurate measurements of Foeq(zm) requires stiff polymers with small L/lp, where L is the contour length of the handle, and lp is the persistence length. Paradoxically, reliable estimates of the hopping rates can only be made by using flexible handles. Nevertheless, we show that the equilibrium free-energy profile Foeq(zm) at an external tension fm, the force (f) at which the folded and unfolded states are equally populated, in conjunction with Kramers' theory, can provide accurate estimates of the force-dependent hopping rates in the absence of handles at arbitrary values of f. Our theoretical framework shows that zm is a good reaction coordinate for nucleic acid hairpins under tension.Changbong HyeonGreg Morrisongreg.morrison@imtlucca.itD. Thirumalai2013-10-04T09:04:06Z2014-12-05T09:21:38Zhttp://eprints.imtlucca.it/id/eprint/1815This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18152013-10-04T09:04:06ZRole of internal chain dynamics on the rupture kinetic of adhesive contactsWe study the forced rupture of adhesive contacts between monomers that are not covalently linked in a
Rouse chain. When the applied force (f) to the chain end is less than the critical force for rupture (fc), the
reversible rupture process is coupled to the internal Rouse modes. If f=fc > 1 the rupture is irreversible.
In both limits, the nonexponential distribution of contact lifetimes, which depends sensitively on the
location of the contact, follows the double-exponential (Gumbel) distribution. When two contacts are well
separated along the chain, the rate limiting step in the sequential rupture kinetics is the disruption of the
contact that is in the chain interior. If the two contacts are close to each other, they cooperate to sustain the
stress, which results in an ‘‘all-or-none’’ transition.Valeri BarsegovGreg Morrisongreg.morrison@imtlucca.itD. Thirumalai2013-10-03T13:31:30Z2016-04-06T10:05:02Zhttp://eprints.imtlucca.it/id/eprint/1814This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18142013-10-03T13:31:30ZStretching HomopolymersForce-induced stretching of polymers is important in a variety of contexts. We have used theory and simulations to describe the response of homopolymers, with N monomers, to an external force (f ) in good and poor solvents. In good solvents and for sufficiently large N we show, in accord with scaling predictions, that the mean extension along the f axis 〈Z〉 ∼ f for small f and 〈Z〉 ∼ f 2/3 (the Pincus regime) for intermediate values of f. The theoretical predictions for 〈Z〉 as a function of f are in excellent agreement with simulations for N = 100 and 1600. However, even with N = 1600, the expected Pincus regime is not observed due to the breakdown of the assumptions in the blob picture for finite N. We predict the Pincus scaling in a good solvent will be observed for N ≳ 105. The force-dependent structure factors for a polymer in a poor solvent show that there is a hierarchy of structures, depending on the nature of the solvent. For a weakly hydrophobic polymer, various structures (ideal conformations, self-avoiding chains, globules, and rods) emerge on distinct length scales as f is varied. A strongly hydrophobic polymer remains globular as long as f is less than a critical value fc. Above fc, an abrupt first-order transition to a rodlike structure occurs. Our predictions can be tested using single molecule experiments. Greg Morrisongreg.morrison@imtlucca.itChangbong HyeonNgo Minh ToanBae-Yeun HaD. Thirumalai2013-10-03T11:24:17Z2013-10-04T11:07:28Zhttp://eprints.imtlucca.it/id/eprint/1813This item is in the repository with the URL: http://eprints.imtlucca.it/id/eprint/18132013-10-03T11:24:17ZThe shape of a flexible polymer in a cylindrical poreWe calculate the mean end-to-end distance R of a self-avoiding polymer encapsulated in an infinitely long cylinder with radius D. A self-consistent perturbation theory is used to calculate R as a function of D for impenetrable hard walls and soft walls. In both cases, R obeys the predicted scaling behavior in the limit of large and small D. The crossover from the three-dimensional behavior (D→∞) to the fully stretched one-dimensional case (D→0) is nonmonotonic. The minimum value of R is found at D ∼ 0.46RF, where RF is the Flory radius of R at D→∞. The results for soft walls map onto the hard wall case with a larger cylinder radius.Greg Morrisongreg.morrison@imtlucca.itD. Thirumalai