Topological optimization for tailored designs of advection–diffusion-reaction porous reactors based on pore scale modeling and simulation: A PNM-NSGA framework

Alizadeh Mehrzad, Gostick Jeff, Suzuki Takahiro, et al. Topological optimization for tailored designs of advection–diffusion-reaction porous reactors based on pore scale modeling and simulation: A PNM-NSGA framework. Computers & Structures 301, 107452 (2024); https://doi.org/10.1016/j.compstruc.2024.107452

Quantitative Protein Dynamics from Dominant Folding Pathways

We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding problem are removed and simulating the entire reaction in atomistic details using existing computers becomes feasible. In addition, this formalism provides a natural framework to investigate the relationships between thermodynamical and kinetic aspects of the folding. For example, it is possible to show that, in order to have a large probability to remain unchanged under Langevin diffusion, the native state has to be characterized by a small conformational entropy. We discuss how to determine the most probable folding pathway, to identify configurations representative of the transition state and to compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine di-peptide, within an all-atom model based on the empiric GROMOS96 force field.Comment: 4 pages, 1 figur

Computational Modalities of Belousov-Zhabotinsky Encapsulated Vesicles

We present both simulated and partial empirical evidence for the computational utility of many connected vesicle analogs of an encapsulated non-linear chemical processing medium. By connecting small vesicles containing a solution of sub-excitable Belousov-Zhabotinsky (BZ) reaction, sustained and propagating wave fragments are modulated by both spatial geometry, network connectivity and their interaction with other waves. The processing ability is demonstrated through the creation of simple Boolean logic gates and then by the combination of those gates to create more complex circuits

On computing in fine-grained compartmentalised Belousov-Zhabotinsky medium

We introduce results of computer experiments on information processing in a hexagonal array of vesicles filled with Belousov-Zhabotinsky (BZ) solution in a sub-excitable mode. We represent values of Boolean variables by excitation wave-fragments and implement basic logical gates by colliding the wave-fragments. We show that a vesicle filled with BZ mixture can implement a range of basic logical functions. We cascade BZ-vesicle logical gates into arithmetic circuits implementing addition of two one-bit binary numbers. We envisage that our theoretical results will be applied in chemical laboratory designs of massive-parallel computers based on fine-grained compartmentalisation of excitable chemical systems