Related papers: A Two-Step Biopolymer Nucleation Model Shows a Non…
Biomolecules composed of a limited set of chemical building blocks can co-localize into distinct, spatially segregated compartments known as biomolecular condensates. While many condensates are known to form spontaneously via phase…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Phase separation drives the formation of biomolecular condensates in cells, which comprise many components and sometimes possess multiple phases. The equilibrium physics of phase separation is well understood, but many components in…
We present theory and simulation of simultaneous chemical demixing and phase ordering in a polymer-liquid crystal mixture in conditions where isotropic-isotropic phase separation is metastable with respect to isotropic-nematic phase…
Non-equilibrium clustering and percolation are investigated in an archetypal model of two-dimensional active matter using dynamic simulations of self-propelled Brownian repulsive particles. We concentrate on the single-phase region up to…
Motivated by results from an earlier Brownian Dynamics (BD) simulation for the collapse of a single, stiff polymer in a poor solvent [B. Schnurr, F. C. MacKintosh, and D. R. M. Williams, Europhys. Lett. 51 (3), 279 (2000)] we calculate the…
A new model that includes the time-dependent dynamics of the single-particle (s.p.) motion in conjunction with the macroscopic evolution of the system is proposed for describing the compound nucleus (CN) formation in fusion of heavy nuclei.…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of…
We study the critical phenomena of the dynamical transition from a metastable state to a stable state in the model of first-order phase transition via two different triggering mechanisms. Three universal stages during the fully nonlinear…
Within self-consistent field theory we study the phase behavior of a symmetrical binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A…
Geopolymers are an emerging class of binding materials used in sustainable cements, concretes, and composites. However, despite growing research, the lack of standardised processes and stability analyses for formulating activator solutions…
Block copolymer (BCP) melt assembly has been the subject of decades of study, with focus largely on self-organized spatial patterns of periodically-ordered segment density. In this study, we demonstrate that underlying these otherwise…
Dual phospho/dephosphorylation cycles, as well as covalent enzymatic-catalyzed modifications of substrates, are widely diffused within cellular systems and are crucial for the control of complex responses such as learning, memory and…
We study a class of models for \sbentcore molecules using low density version of Local Density Functional Theory. Arms of the molecules are modeled using two- and three Gay-Berne (GB) interacting units of uniaxial and biaxial symmetry.…
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerisation has been studied theoretically in a number of contexts, often by considering a Markov process in…
We present a systematic framework for shortening and automating molecular dynamics equilibration through improved position initialization methods and uncertainty quantification analysis, using the Yukawa one-component plasma as an exemplar…
Metastable phases can lead to multistep nucleation processes, influencing the liquid-to-solid transition in various systems. In this study, we investigate the homogeneous nucleation of iron's crystalline phases under Earth's inner core…
Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different…