Related papers: Improved prediction of molecular response to pulli…
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
A data fitting procedure is devised and thoroughly tested to provide self-consistent estimates of the relevant mechanokinetic parameters involved in a plausible scheme underpinning the output of an ensemble of myosin II molecular motors…
Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to…
Cells within biological tissue are constantly subjected to dynamic mechanical forces. Measuring the internal stress of tissues has proven crucial for our understanding of the role of mechanical forces in fundamental biological processes…
Novel physical mechanism is proposed for explanation of temperature-independent transition reactions in molecular systems. The mechanism becomes effective in the case of conformation transitions between quasi-isoenergetic molecular states.…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
Sampling Boltzmann probability distributions plays a key role in machine learning and optimization, motivating the design of hardware accelerators such as Ising machines. While the Ising model can in principle encode arbitrary optimization…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Predicting transcriptional responses to novel drugs provides a unique opportunity to accelerate biomedical research and advance drug discovery efforts. However, the inherent complexity and high dimensionality of cellular responses, combined…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
Traction Force Microscopy (TFM) is a technique used to determine the tensions that a biological cell conveys to the underlying surface. Typically, TFM requires culturing cells on gels with fluorescent beads, followed by bead displacement…
It has been reported recently that the equipartition theorem is violated in molecular dynamics simulations with periodic boundary condition [Shirts et al, J. Chem. Phys. 125, 164102 (2006)]. This effect is associated with the conservation…
To address the computational challenges of ab initio molecular dynamics and the accuracy limitations of empirical force fields, the introduction of machine learning force fields has proven effective in various systems including metals and…
An approach to the mechanical behaviour of textile composites at the scale of their constituting fibres, using an implicit finite element simulation code, is proposed in this chapter. The approach is based on efficient methods and…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
Atmosphere modelling applications become increasingly memory-bound due to the inconsistent development rates between processor speeds and memory bandwidth. In this study, we mitigate memory bottlenecks and reduce the computational load of…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…