Related papers: Rebinding kinetics from single-molecule force spec…
A major obstacle for computing optical spectra of solids is the lack of reliable approximations for capturing excitonic effects within time-dependent density-functional theory. We show that the trustful prediction of strongly bound…
We present molecular dynamics simulations on the structural relaxation of a simple bead-spring model for polymer blends. The introduction of a different monomer size induces a large time scale separation for the dynamics of the two…
Machine learning is used to approximate the kinetic energy of one dimensional diatomics as a functional of the electron density. The functional can accurately dissociate a diatomic, and can be systematically improved with training. Highly…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
Probability estimation by maximum entropy reconstruction of an initial relative frequency estimate from its projection onto a hypergraph model of the approximate conditional independence relations exhibited by it is investigated. The…
In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers, and the total extension -- of molecule plus apparatus -- is monitored as a function of time. In a typical unfolding…
We discuss the physics and modeling of latex-rubber slingshots. The goal is to get accurate speed predictions inspite of the significant real world difficulties of force drift, force hysteresis, rubber ageing, and the very non- linear,…
The concept of valence bond resonance plays a fundamental role in the theory of the chemical bond and is believed to lie at the heart of many-body quantum physical phenomena. Here we show direct experimental evidence of a time-resolved…
We consider the fracture of a free-standing two-dimensional (2D) elastic-brittle network to be used as protective coating subject to constant tensile stress applied on its rim. Using a Molecular Dynamics simulation with Langevin thermostat,…
Constituent quark models, while successful, require a great deal of fine tuning of the short distance interactions by introducing phenomenological gluonic form factors which are ultimately designed to accurately reproduce the spectrum. We…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Biomolecular binding kinetics including the association (kon) and dissociation (koff) rates are critical parameters for therapeutic design of small-molecule drugs, peptides and antibodies. Notably, drug molecule residence time or…
We report the experimental generation of all four frequency-bin Bell states in a single versatile setup via successive pumping of spontaneous parametric downconversion with single and dual spectral lines. Our scheme utilizes intensity…
We solve the stochastic equations for a cluster of parallel bonds with shared constant loading, rebinding and the completely dissociated state as an absorbing boundary. In the small force regime, cluster lifetime grows only logarithmically…
We discuss the force-velocity relations obtained in a two-state crossbridge model for molecular motors. They can be calculated analytically in two limiting cases: for a large number and for one pair of motors. The effect of the…
Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…
We develop a kinetic-theory framework to investigate the steady rheology of a dilute gas interacting via a repulsive potential under uniform shear flow. Starting from the Boltzmann equation with a restitution coefficient that depends on the…
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica…
We apply statistical mechanics to an inverse problem of linear mapping to investigate the physics of the irreversible compression. We use the replica symmetry breaking (RSB) technique with a toy model to demonstrate the Shannon's result.…