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Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal…
We study kinetics of single species reactions ("A+A -> 0") for general local reactivity Q and dynamical exponent z (rms displacement x_t ~ t^{1/z}.) For small molecules z=2, whilst z=4,8 for certain polymer systems. For dimensions d above…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication,…
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…
Spatiotemporal pattern formation in a product-activated enzymic reaction at high enzyme concentrations is investigated. Stochastic simulations show that catalytic turnover cycles of individual enzymes can become coherent and that complex…
The kinetics of dislocation reactions, such as dislocation multiplication, controls the plastic deformation in crystals beyond their elastic limit, therefore critical mechanisms in a number of applications in materials science. We present a…
The computer-assisted modeling of re-entrant production lines, and, in particular, simulation scalability, is attracting a lot of attention due to the importance of such lines in semiconductor manufacturing. Re-entrant flows lead to…
Microscopic models of reaction-diffusion processes on the cell membrane can link local spatiotemporal effects to macroscopic self-organized patterns often observed on the membrane. Simulation schemes based on the microscopic lattice method…
The run and tumble process is well established in order to describe the movement of bacteria in response to a chemical stimulus. However the relation between the tumbling rate and the internal state of bacteria is poorly understood. The…
Various kinetic Monte Carlo algorithms become inefficient when some of the population sizes in a system are large, which gives rise to a large number of reaction events per unit time. Here, we present a new acceleration algorithm based on…
Electrochemical devices often consist of multicomponent electrolyte solutions. Two processes influence the overall dynamics of these devices: the formation of electrical double layers and chemical conversion due to redox reactions. However,…
Cells can use periodic enzyme activities to adapt to periodic environments or existing internal rhythms and to establish metabolic cycles that schedule biochemical processes in time. A periodically changing allocation of the protein budget…
We study long-range interacting systems perturbed by external stochastic forces. Unlike the case of short-range systems, where stochastic forces usually act locally on each particle, here we consider perturbations by external stochastic…
The problem of observing rare events is pervasive among the molecular dynamics community and an array of different types of methods are commonly used to accelerate these long timescale processes. Typically, rare event acceleration methods…
We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order O(N), where $N$ is the number of particles. The algorithm works very effectively when the particles…