Related papers: Single molecule pulling with large time steps
Tracking experiments in dense biological tissues reveal a diversity of sources f or local energy injection at the cell scale. The effect of cell motility has been largely studied, but much less is known abo ut the effect of the observed…
Homogeneous nucleation and growth in a simplest two-dimensional phase field model is numerically studied using the cell dynamics method. Whole process from nucleation to growth is simulated and is shown to follow closely the…
Theories that are used to extract energy-landscape information from single-molecule pulling experiments in biophysics are all invariably based on Kramers' theory of thermally-activated escape rate from a potential well. As is well known,…
We apply a recent proposal for defining states and observables in quantum gravity to simple models. First, we consider a Klein-Gordon particle in an ex- ternal potential in Minkowski space and compare our proposal to the theory ob- tained…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
We study the force-induced unfolding of a homopolymer on the three dimensional Sierpinski gasket. The polymer is subject to a contact energy between nearest neighbour sites not consecutive along the chain and to a stretching force. The…
We study the properties of convex functionals which have been proposed for the simulation of charged molecular systems within the Poisson-Boltzmann approximation. We consider the extent to which the functionals reproduce the true…
To quantify the progress in development of algorithms and forcefields used in molecular simulations, a method for the assessment of the sampling quality is needed. We propose a general method to assess the sampling quality through the…
Accurate, yet computationally efficient energy functions are essential for state-of-the art molecular dynamics (MD) studies of condensed phase systems. Here, a generic workflow based on a combination of machine learning-based and empirical…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
The dynamics of a particle coupled to a dense and homogeneous ideal Fermi gas in two spatial dimensions is studied. We analyze the model for coupling parameter g=1 (i.e., not in the weak coupling regime), and prove closeness of the time…
Numerous upcoming observations, such as WFIRST, BOSS, BigBOSS, LSST, Euclid, and Planck, will constrain dark energy (DE)'s equation of state with great precision. They may well find the ratio of pressure to energy density, $w$, is -1,…
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…
We consider a self-avoiding walk model of polymer adsorption where the adsorbed polymer can be desorbed by the application of a force, concentrating on the case of the square lattice. Using series analysis methods we investigate the…
Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…
Phase field crystals (PFC) are a tool for simulating materials at the atomic level. They combine the small length-scale resolution of molecular dynamics (MD) with the ability to simulate dynamics on mesoscopic time scales. We show how PFC…
Phase separation plays an role in determining the self-assembly of biological and soft-matter systems. In biological systems, liquid-liquid phase separation inside a cell leads to the formation of various macromolecular aggregates. The…
Fusion power plants will require detachment to mitigate sputtering and keep divertor heat fluxes at tolerable levels. Controlling detachment on these devices may require the use of real-time scrape-off-layer modeling to complement the…
In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs:…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…