Related papers: The Mesoscopic Partition Function:A Combined Spati…
The mesoscopic concept is a way to deal with complex materials with an internal structure within continuum mechanics. It consists of extending the domain of the balance equations by mesoscopic variables and of introducing a local…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
Mesoscopic theory for self-assembling systems near a planar confining surface is developed. Euler- Lagrange (EL) equations and the boundary conditions (BC) for the local volume fraction and the correlation function are derived from the DFT…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse-graining affects entropy and dissipation, two factors enter the rescaling:…
We introduce the notion of cell division-induced activity and show that the cell division generates extensile forces and drives dynamical patterns in cell assemblies. Extending the hydrodynamic models of lyotropic active nematics we…
One aim of the equal load sharing fiber bundle model is to describe the critical behavior of failure events. One way of accomplishing this, is through a discrete recursive dynamics. We introduce a continuous mesoscopic equation catching the…
The conventional phase space of classical physics treats space and time differently, and this difference carries over to field theories and quantum mechanics (QM). In this paper, the phase space is enhanced through two main extensions.…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
The subject of this paper is the evolution of the concept of information processing in regular structures based on multi-level processing in nested cellular automata. The essence of the proposed model is a discrete space-time containing…
Cell sorting, the segregation of cells with different properties into distinct domains, is a key phenomenon in biological processes such as embryogenesis. We use a phase-field model of a confluent cell layer to study the role of activity in…
We study the partition function associated with the democratic formulation of M-theory, focusing on its global definition and quantum properties. Using a path-integral representation that makes manifest the underlying cohomological…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
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…
We develop a systematic coarse graining procedure for systems of $N$ qubits. We exploit the underlying geometrical structures of the associated discrete phase space to produce a coarse-grained version with reduced effective size. Our…