Related papers: Metabolism, information, and viability in a simula…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
We explore electron transport properties for the model of benzene-1, 4-dithiolate (BDT) molecule and for some other geometric models of benzene molecule attached to two semi-infinite one-dimensional metallic electrodes using the Green's…
Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…
The quantum network model with real variables is usually used to describe the excitation energy transfer (EET) in the Fenna-Matthews-Olson(FMO) complexes. In this paper we add the quantum phase factors to the hopping terms and find that the…
There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
Signal transduction, or signal-processing capability, is a fundamental property of nature that manifests universally across systems of different scales -- from quantum behaviour to the biological. This includes the detection of…
As the first step in an investigation of the origin of genetic information, we study how some species of molecules are preserved over cell generations and play an important role in controlling the growth of a cell. We consider a model…
Redox molecular junctions are molecular conduction junctions that involve more than one oxidation state of the molecular bridge. This property is derived from the ability of the molecule to transiently localize transmitting electrons,…
In many biological systems, the movement of individual agents is commonly characterized as having multiple qualitatively distinct behaviors that arise from various biophysical states. This is true for vesicles in intracellular transport,…
Function in natural systems arises from one-dimensional sequences forming three-dimensional structures with specific properties. However, current generative models suffer from critical limitations: training objectives seldom target function…
Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium…
Shuttle-assisted charge transfer is pivotal for the efficient energy transduction from the food-stuff electrons to protons in the respiratory chain of animal cells and bacteria. The respiratory chain consists of four metalloprotein…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
This paper proposes a latent prompt Transformer model for solving challenging optimization problems such as molecule design, where the goal is to find molecules with optimal values of a target chemical or biological property that can be…
We simulate the long-range inter-complex electronic energy transfer in Photosystem II -- from the antenna complex, via a core complex, to the reaction center -- using a non-Markovian (ZOFE) quantum master equation description that allows us…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…