相关论文: Optimal flexibility for conformational transitions…
Biological macromolecules have complex and non-trivial energy landscapes, endowing them a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
The speed of integrated circuits is ultimately limited by the mobility of electrons or holes, which depend on the effective mass in a semiconductor. Here, building on an analogy with electromagnetic metamaterials and transformation optics,…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
Sequence modelling requires determining which past tokens are causally relevant from the context and their importance: a process inherent to the attention layers in transformers, yet whose underlying learned mechanisms remain poorly…
Building on the recently derived inhomogeneous mode-coupling theory, we extend the generalised mode-coupling theory of supercooled liquids to inhomogeneous environments. This provides a first-principles-based, systematic and rigorous way of…
We study the control by electromagnetic fields of molecular alignment and orientation, in a linear, rigid rotor model. With the help of a monotonically convergent algorithm, we find that the optimal field is in the microwave part of the…
We study slow dynamics of particles moving in a matrix of immobile obstacles using molecular dynamics simulations. The glass transition point decreases drastically as the obstacle density increases. At higher obstacle densities, the…
Chemotaxis and haptotaxis have been a main theme in the macroscopic study of bacterial and cellular motility. In this work we investigate the influence these processes have on the shape and motility of fast migrating cells. We note that…
The key to understanding a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility and function of…
A new type of a capacitor with a very high volumetric capacitance is proposed. It is based upon the known phenomenon of a sharp increase of the dielectric constant of the metal-insulator composite in the vicinity of the percolation…
Cell dynamics simulation is used to investigate the phase behavior of block copolymer/homopolymer mixture subjected to a steady shear flow. Phase transitions occur from transverse to parallel and then to perpendicular lamellar structure…
To optimize the design of STT-MRAM (spin-transfer torque magnetic random access memory), it is necessary to be able to predict switching (error) rates. For small elements, this can be done using a single-macrospin theory since the element…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
If quenched fast enough, a liquid is able to avoid crystallization and will remain in a metastable supercooled state down to the glass transition, with an important increase in viscosity upon further cooling. There are important differences…
Cells make use of semi-flexible biopolymers such as actin or intermediate filaments to control their local viscoelastic response by dynamically adjusting the concentration and type of cross-linker molecules. The microstructure of the…
A nonlinear continuum theory is advanced for high-rate mechanics and thermodynamics of liver parenchyma. The homogenized continuum is idealized as a solid-fluid mixture of dense viscoelastic tissue and liquid blood. The solid consists of a…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…