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The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient…
This paper presents a novel event camera simulation system fully based on physically based Monte Carlo path tracing with adaptive path sampling. The adaptive sampling performed in the proposed method is based on a statistical technique,…
Fibers of bent-core liquid crystals present an internal structure of a rolled smectic layer and can be used as optical waveguides. We used a field-theoretical Monte Carlo simulation to analyze the internal configuration of such fibers as a…
We present a new algorithm for radiative transfer-based on a statistical Monte Carlo approach-that does not suffer from teleportation effects, on the one hand, and yields smooth results, on the other hand. Implicit Monte Carlo (IMC)…
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…
The monolayer adsorption process of interacting binary mixtures of species $A$ and $B$ on square lattices is studied through grand canonical Monte Carlo simulation in the framework of the lattice-gas model. Four different energies have been…
Transmission matrices, mapping the propagation of light from one end of the tissue to the other, form an important mathematical tool in the analysis of tissue scattering and the design of wavefront shaping systems. To understand the…
We present a new efficient method for Monte Carlo simulations of diffusion-reaction processes. First introduced by us in [Phys. Rev. Lett., 97:230602, 2006], the new algorithm skips the traditional small diffusion hops and propagates the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and…
Indirect imaging problems in biomedical optics generally require repeated evaluation of forward models of radiative transport, for which Monte Carlo is accurate yet computationally costly. We develop a novel approach to reduce this…
A discrete model for computer simulations of the clustering dynamics of Social Amoebae is presented. This model incorporates the wavelike propagation of extracellular signaling cAMP, the sporadic firing of cells at early stage of…
Dynamic phase transition phenomena in ultrathin films described by Blume-Capel model have been investigated using Monte Carlo simulations. Hysteresis loops, micromagnetic structures, and hysteresis loop area curves, as well as dynamic…
Monte Carlo radiative transfer, which has been demonstrated as a successful algorithm for modeling radiation transport through the astrophysical medium, relies on sampling of scattering phase functions. We review several classic sampling…
A real-time path integral Monte Carlo approach is developed to study the dynamics in a many-body quantum system until reaching a nonequilibrium stationary state. The approach is based on augmenting an exact reduced equation for the…
We propose a method for Monte Carlo simulations of systems with a complex action. The method has the advantages of being in principle applicable to any such system and provides a solution to the overlap problem. We apply it in random matrix…
With the increasing precision requirements and growing spectrum of applications of Monte Carlo simulations the evaluation of different components of such simulations and their systematic ambiguities become of utmost interest. In the…
An indirect, hybrid Monte Carlo discretization of general relativistic kinetic theory suitable for the development of numerical schemes for radiation transport is presented. The discretization is based on surface flux estimators obtained…