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It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
In this article, we describe a recursive method to construct a subset of relevant Slater-determinants for the use in many-body diagonalization schemes that will be employed in our forthcoming papers on the simulation of excited many-body…
Droplet interface bilayers are a convenient model system to study the physio-chemical properties of phospholipid bilayers, the major component of the cell membrane. The mechanical response of these bilayers to various external mechanical…
We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure.…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
Abundant in nature, colloids also find increasingly important applications in science and technology, ranging from direct probing of kinetics in crystals and glasses to fabrication of third-generation quantum-dot solar cells. Because…
2D conjugated polyphthalocyanines can be obtained as two distinctly different types of material with specific molecular structures and different morphological properties. It was believed that the temperature is the key factor affecting the…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our…
Understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step towards unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. We use…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
Biological systems are non-linear, include unobserved variables and the physical principles that govern their dynamics are partly unknown. This makes the characterization of their behavior very challenging. Notably, their activity occurs on…
For problems in astrophysics, planetary science and beyond, numerical simulations are often limited to simulating fewer particles than in the real system. To model collisions, the simulated particles (aka superparticles) need to be inflated…
Soft matter systems are common in nature and make up nearly all the essential components necessary for life, from cells to the organelles within those cells. The ability of these soft materials to deform is crucial for the proper…
In particle-in-cell simulations, excessive or even unfeasible computational demands can be caused by the growth of the number of particles in the course of prolific ionization or cascaded pair production due to the effects of quantum…
Inspired by a PDE-ODE system of aggregation developed in the biomathematical literature, an interacting particle system representing aggregation at the level of individuals is investigated. It is proved that the empirical density of the…
A high-performance p-type transparent conductor (TC) does not yet exist, but could lead to advances in a wide range of optoelectronic applications and enable new architectures for, e.g., next-generation photovoltaic (PV) devices.…
In this paper, Particle-in-Cell algorithms for the Vlasov-Poisson system are presented based on its Poisson bracket structure. The Poisson equation is solved by finite element methods, in which the appropriate finite element spaces are…
We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic…