Related papers: The study of water shell structure of double-helic…
We wish to suggest an algorithm for biological search including DNA search. Our argument supposes that biological search be performed by quantum search.If we assume this, we can naturally answer the following long lasting puzzles such that…
Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A. Modern…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
In the frameworks of algebraic topology {\alpha}-helix and different DNA-conformations are determined as the local latticed packing, confined by peculiar minimal surfaces which are similar to helicoids. These structures are defined by…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
We introduce a shell-model theory that combines traditional spherical states, which yield a diagonal representation of the usual single-particle interaction, with collective configurations that track deformations, and test the validity of…
The self-assembly of DNA-coated colloids controlled by enzymatic reactions has the potential to enable the formation of materials with hierarchical organization and switchable configurations. However, the problem of designing such…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…
A survey is given on the applications of hydrodynamic model of nucleus-nucleus collisons, focusing especially on i) the resolution of hydrodynamic equations for arbitrary configurations, by using the smoothed-particle hydrodynamic approach;…
We discuss the present status of the description of the structure of the very neutron rich nuclei, in the framework of modern large scale shell model calculations. Particular attention is paid to the interaction related issues, as well as…
There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms which play a crucial role in electrochemistry and biology. In this study, the…
It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are…
Deep learning has become a powerful tool in computational biology, revolutionising the analysis and interpretation of biological data over time. In our article review, we delve into various aspects of deep learning in computational biology.…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
Theoretical and experimental investigations of water vapor interaction with porous materials are very needful for various fields of science and technology. Not only studies of the interaction of water vapor and porous material as a…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The patterns arising from the differential swelling of gels are investigated experimentally and theoretically as a model for the differential growth of living tissues. Two geometries are considered: a thin strip of soft gel clamped to a…
We revisit the long-standing question of whether water molecules dissociate on the Ru(0001) surface through nanosecond-scale path-integral molecular dynamics simulations on a sizable supercell. This is made possible through the development…
A new code for nuclear shell-model calculations, "KSHELL", is developed. It aims at carrying out both massively parallel computation and single-node computation in the same manner. We solve the Schr\"{o}dinger's equation in the $M$-scheme…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…