Search Results - "Niemi, Antti J."

Poincaré index formula and analogy with the Kosterlitz-Thouless transition in a non-rotated cold atom Bose-Einstein condensate by Garaud, Julien, Niemi, Antti J.

“…A bstract A dilute gas of Bose-Einstein condensed atoms in a non-rotated and axially symmetric harmonic trap is modelled by the time dependent Gross-Pitaevskii…”
Get full text

Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example by Peng, Xubiao, Niemi, Antti J

“…Novel topological methods are introduced to protein research. The aim is to identify hot-spot sites where a bifurcation can alter the local topology of the…”
Get full text

Provenance of classical Hamiltonian time crystals by Alekseev, Anton, Dai, Jin, Niemi, Antti J.

“…A bstract Classical Hamiltonian systems with conserved charges and those with constraints often describe dynamics on a pre-symplectic manifold. Here we show…”
Get full text

Vortex precession and exchange in a Bose-Einstein condensate by Garaud, Julien, Dai, Jin, Niemi, Antti J.

“…A bstract Vortices in a Bose-Einstein condensate are modelled as spontaneously symmetry breaking minimum energy solutions of the time dependent…”
Get full text

Rotation by deformation and time-crystalline dynamics of cyclopropane molecule by Peng, Xubiao, Dai, Jin, Niemi, Antti J

“…A deformable body can rotate even with no angular momentum simply by changing its shape. Here the first all-atom level molecular dynamics example of this…”
Get full text

Classical Hamiltonian time crystals-general theory and simple examples by Dai, Jin, Niemi, Antti J, Peng, Xubiao

“…We focus on a Hamiltonian system with a continuous symmetry, and dynamics that takes place on a presymplectic manifold. We explain how the symmetry can become…”
Get full text

On topology and knotty entanglement in protein folding by Begun, Alexander, Liubimov, Sergei, Molochkov, Alexander, Niemi, Antti J

“…We investigate aspects of topology in protein folding. For this we numerically simulate the temperature driven folding and unfolding of the slipknotted…”
Get full text

Study of correlations between protein peptide plane dynamics and side chain dynamics by Hou, Yanzhen, Liu, Jiaojiao, He, Jianfeng, Peng, Xubiao, Niemi, Antti J

“…Protein dynamics is pivotal to biological processes. However, experiments are very demanding and difficult to perform, and all-atom molecular dynamics…”
Get full text

Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach by Liwo, Adam, Pyrka, Maciej, Czaplewski, Cezary, Peng, Xubiao, Niemi, Antti J

“…Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly…”
Get full text

Stable knot-like structures in classical field theory by Faddeev, L, Niemi, Antti J

Get full text

Topological Indices of Proteins by Melnikov, Dmitry, Niemi, Antti J., Sedrakyan, Ara

“…Protein molecules can be approximated by discrete polygonal chains of amino acids. Standard topological tools can be applied to the smoothening of the polygons…”
Get full text

Discrete nonlinear Schrödinger equation and polygonal solitons with applications to collapsed proteins by Molkenthin, Nora, Hu, Shuangwei, Niemi, Antti J

“…We introduce a novel generalization of the discrete nonlinear Schrödinger equation. It supports solitons that we utilize to model chiral polymers in the…”
Get full text

Exploring Structural Flexibility and Stability of α-Synuclein by the Landau–Ginzburg–Wilson Approach by Korneev, Anatolii, Begun, Alexander, Liubimov, Sergei, Kachlishvili, Khatuna, Molochkov, Alexander, Niemi, Antti J., Maisuradze, Gia G.

“…α-Synuclein (αS) is the principal protein component of the Lewy body and Lewy neurite deposits that are found in the brains of the victims of one of the most…”
Get full text

Protein tertiary structure and the myoglobin phase diagram by Begun, Alexander, Molochkov, Alexander, Niemi, Antti J.

“…We develop an effective theory approach to investigate the phase properties of globular proteins. Instead of interactions between individual atoms or localized…”
Get full text

A comparison of reduced coordinate sets for describing protein structure by Hinsen, Konrad, Hu, Shuangwei, Kneller, Gerald R, Niemi, Antti J

“…In all-atom molecular simulation studies of proteins, each atom in the protein is represented by a point mass and interactions are defined in terms of the…”
Get more information

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics by Sieradzan, Adam K, Korneev, Anatolii, Begun, Alexander, Kachlishvili, Khatuna, Scheraga, Harold A, Molochkov, Alexander, Senet, Patrick, Niemi, Antti J, Maisuradze, Gia G

“…Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to…”
Get full text

Can the geometry of all-atom protein trajectories be reconstructed from the knowledge of Cα time evolution? A study of peptide plane O and side chain Cβ atoms by Liu, Jiaojiao, Dai, Jin, He, Jianfeng, Peng, Xubiao, Niemi, Antti J

“…We inquire to what extent can the geometry of protein peptide plane and side chain atoms be reconstructed from the knowledge of Cα time evolution. Due to the…”
Get more information

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain by Kachlishvili, Khatuna, Korneev, Anatolii, Maisuradze, Luka, Liu, Jiaojiao, Scheraga, Harold A, Molochkov, Alexander, Senet, Patrick, Niemi, Antti J, Maisuradze, Gia G

“…Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases…”
Get full text

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics by Krokhotin, Andrey, Niemi, Antti J, Peng, Xubiao

“…We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the…”
Get more information

Myoglobin ligand gate mechanism analysis by a novel 3D visualization technique by Hou, Yanzhen, Niemi, Antti J., Peng, Xubiao, Ilieva, Nevena

“…A protein is commonly visualized as a discrete piecewise linear curve, conventionally characterized in terms of the extrinsically determined Ramachandran…”
Get full text