Related papers: Towards Experimental P-systems using multivesicula…
In this paper we investigate the number of objects actually used in the terminating computations of a certain variant of polarizationless P systems with active membranes. The P systems we consider here have no in-communication rules and…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
Inspired by the emergent membrane computing (P Systems) concepts, some efforts are carried out introducing simulation models, some are software oriented, and others are hardware, yet all are applied with the current vision of the…
Particle-in-Cell (PIC) simulation codes have wide applicability to first-principles modeling of multidimensional nonlinear plasma phenomena, including wake-field accelerators. This review addresses both finite difference and pseudo-spectral…
Ionic liquids are widely used as electrolytes in electrochemical devices. In this context, many experimental and theoretical approaches have been recently developed for characterizing their interface with electrodes. In this perspective…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Cells offer numerous inspiring examples where proteins and membranes combine to form complex structures that are key to intracellular compartmentalization, cargo transport, and specialization of cell morphology. Despite this wealth of…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
Probabilistic integral circuits (PICs) have been recently introduced as probabilistic models enjoying the key ingredient behind expressive generative models: continuous latent variables (LVs). PICs are symbolic computational graphs defining…
Artificial bilayer lipid membranes (BLMs), along with patch-clamped membranes, are frequently used for functional analyses of membrane proteins. In both methods, the electric properties of membranes are characterized by only one parameter,…
We introduce quantum circuits for simulations of multi-mode state-vectors on 3D cQED processors, using matrix product state representations. The circuits are demonstrated as applied to simulations of molecular docking based on holographic…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
Collective modes of doped two-dimensional crystalline materials, namely graphene, MoS$_2$ and phosphorene, both monolayer and bilayer structures, are explored using the density functional theory simulations together with the random phase…
This study introduces an open-source computational framework for the generation and permeability evaluation of synthetic porous media. The proposed methodology integrates crystallographic and meshing tools to construct controlled…
This postdoctoral thesis starts by reviewing the historic development of airplane structures and high lift devices from an engineering point of view. However, the main purpose of this document is the development of a novel concept for shape…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
We revisit the Scovel-Weinstein framework (Scovel & Weinstein, CPAM 1994) for reducing the Vlasov-Poisson system while preserving its Hamiltonian structure. Standard particle-in-cell (PIC) algorithms approximate the distribution function by…
We describe a concept that has the potential to change how we think about the underlying mechanisms of cell membrane electroporation (EP). Prior experimental, theoretical and modeling have emphasized a single pore lifetime as adequate for…
Since the lipid raft model was developed at the end of the last century, it became clear that the specific molecular arrangements of phospholipid assemblies within a membrane have profound implications in a vast range of physiological…