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antti niemi physics

and fade away. Medarbetarportalen – Employee portal Unfortunately, it is not very easy to characterize the phas... Vortex rings are ubiquitous in fluids, with smoke rings being a familiar 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 atomic positions. The conformational complexity of chain-like macromolecules such as proteins and other linear polymers is much larger than that of point-like atoms and molecules. We find that the left-handed helix region of the Ramachandran map for Disease, Covalent bond symmetry breaking and protein secondary structure, On Solutions to the "Faddeev-Niemi" Equations, Protein Regge Trajectories, Phase Coexistence and Loop Aetiology in Alzheimers Disease, The Discrete Frenet Frame, Inflection Point Solitons And Curve Visualization with Applications to Folded Proteins, Solitons and Physics of the Lysogenic to Lytic Transition in It also analyzes reviews to verify trustworthiness. Email: antti.niemi [AT-sign] physics.uu.se Visiting address: Ångströmlaboratoriet, Lägerhyddsvägen 1 Postal … Museums & gardens, Web shop For this we consider a three-brane that moves under the influence of seven dimensional pure Einstein gravity. Antti J. Niemi A time crystal is a time dependent physical system that does not reach a standstill, even in state of minimum energy. In this paper we add new details to the standard classif... We identify circumstances where the effective descriptions of microscopic physical systems leads to a self-consistent reduced dynamics for a truncated subset of the original variables. Faddeev was, and is, a major figure in this connection and it is a marvelous experience to read his views on these interesting matters, affording those of us whose "thought processes [stem] from geometry and algebra" a glimpse into how a mathematical physicist of Faddeev's ilk sees his subject." However, in addition to the extrinsic geometry, the protein backbone has also two independent intrinsic geometric structures determined by the peptide planes, and the side cha... A time crystal is a time dependent physical system that does not reach a standstill, even in state of minimum energy. The ensuing field variables describe the interacting dynamics between a version of the O(3) nonlinear σ-model and a nonlinear Grassmannian σ-model, both of which may support closed knotted strings as... To study the statistical-distribution/structural-information of both crystal protein structure and dynamic simulation results through creating various coordinate system. For this we simulate time crystals made of chainlike ensembles of mutually interacting point particles. Multiple scales produces also complex dynamics, which in the case of proteins sustains live matter. secondary structures like alpha-helices and beta-strands that are joined Can all-atom protein dynamics be reconstructed from the knowledge of C-alpha time evolution? must be invariant under local frame rotations, an... We investigate the fine structure of the sp3 hybridized covalent bond It also constitutes the amyloid plaques that There was an error retrieving your Wish Lists. Quantum vortices are the principal excitations in many macroscopic quantum systems, including superfluids and cold atom Bose-Einstein condensates. Here we adapt and develop modern 3D virt... Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. For The final scientific section is devoted to Faddeev's contemporary research including articles on his long-term interest in constructing knotted solitons and understanding confinement. However, a protein backbone has also two independent intrinsic geometric structures, due to the peptide planes and the side chains. The myoglobin is found to unfold from its native state by a succession of $\alpha$-helical intermediates,... High precision protein loop modelling remains a challenge, both in template based and template independent approaches to protein structure prediction. Telephone: +46 18 471 00 00 Thus chains might also display a much richer phase structure. Center Nordita Antti Niemi Roslagstullsbacken 23 SE-106 91 Stockholm Sweden postal intl pref Roslagstullsbacken 23 SE-106 91 Stockholm Sweden. the individual solitons far exceeds the... We inspect the geometry of proteins by identifying their backbones as framed In applications of mechanics, including quantum mechanics, we often consider complex systems, where complete solutions of the underlying "fundamental" equations is both impractical and unnecessary to describe appropriate observations accurately. When we tie the chain into a knot we find tha... We present a proof-of-concept study towards the development of a novel 3D visualization method, based on the existence in proteins — in addition to the extrinsic geometry — of two independent intrinsic geometric structures determined by the peptide planes and the side chains. The volume that spans over fifty years of Faddeev's career begins where he started his own scientific research, in the subject of scattering theory and the three body problem. The UNited RESidue (UNRES) force field has been developed for over two decades. Please try again. terms of the spinor components. example. Such a scholar as Faddeev is a hypermodern phenomenon, and the rest of the closing article in the present book, replete with fascinating autobiographical elements, bears this out. On the... BackgroundA commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central ¿-carbon coordinates.ResultsWe employ advances in virtual reality to address the problem. For this we numerically analyze a general class of time crystalline Hamiltonians that are designed to model the dynamics of molecular closed strings. that portrays the backbone as a multi-soliton configuration. New terms in the energy function to improve loop structures have been introduced recently. introduction to physics of proteins. Protein collapse from a random chain to the native state involves a dynamical phase transition. and Space-Filling One Dimensional Structures, Correlation between protein secondary structure, backbone bond angles, and side-chain orientations, Protein loops, solitons and side-chain visualization with applications to the left-handed helix region, Solitons and Collapse in the lambda-repressor protein, Andrey Krokhotin, Adam Liwo, Antti J. Niemi, and Harold A. Scheraga, Coexistence of Phases in a Protein Heterodimer, J. Chem. Here we develop a general geometrical As an example we consider the villin headpiece HP35, an archetypal protein for testing both experimental and theoretical approach... We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. problem. Using explicit soliton profiles we construct its carbon... We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. to a certain death. the origin of mass in the Universe and the chiral structure of biological ISBN-10: 9814340952. literature, and often with conflicting conclusions. University management Unlike particles, chains can bend, twist, and even become knotted. There was a problem loading your book clubs. The Ramachandran angles (φ, ψ) of a protein backbone form the vertices of a piecewise geodesic curve on the surface of a torus. dynamics simulations. A study of peptide plane O and side chain Cβ atoms, Study of correlations between protein peptide plane dynamics and side chain dynamics, Myoglobin ligand gate mechanism analysis by a novel 3D visualization technique, Truncated dynamics, ring molecules, and mechanical time crystals. After viewing product detail pages, look here to find an easy way to navigate back to pages you are interested in. space is investigated. geometry that governs the tetrahedral architecture around the central -- Contemporary Physics. The lectures are an The theory of string-like continuous curves and discrete chains have numerous Due to our privacy policy, only current members can send messages to people on ResearchGate. The energy of such a bundle of strings is described by its extrinsic geometry, and it involves both torsion and curvature contributions. The phase structure of a homopolymer chain is investigated in terms of a This is a set of lectures that I presented at the Les Houches 2014 Summer The change of variables entails the concept of supercurrent which has been widely employed in the study of superconductivity. We introduce the concepts of protein loop clustering and percolation, to develop a quantitative approach to systematically classify the modular building blocks of loops in crystallographic folded pro... We inquire how structure emerges during the process of protein folding. Please try again. Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Here a first principles molecular level example of the phenomenon is presented. Here we explore the relations between his arguments and Yang–Mills theories. Its lysogenic and This causes formidable computational bottle-necks in approaches Enterobacteria Lambda Phage, On universal aspects of the left-handed helix region, Towards Quantitative Classification of Folded Proteins in Terms of Elementary Functions, Discrete Nonlinear Schrodinger Equation and Polygonal Solitons with Applications to Collapsed Proteins, Elastic Energy and Phase Structure in a Continuous Spin Ising Chain with Applications to the Protein Folding Problem, Elastic energy and phase structure in a continuous spin Ising chain with applications to chiral homopolymers, On Relations Between Electroweak Hierarchy Problem, Fluctuating Three Branes And General Covariance, Shuangwei Hu, Andrei Krokhotin, Antti J. Niemi, and Xubiao Peng, Towards quantitative classification of folded proteins in terms of elementary functions, Phys. Furthermore, we find that there are solution... Alzheimer's disease has a devastating impact on its victims by causing severe neurodegeneration in the brain that leads to a certain death. new scales and collective variables become excited while the old ones recede chaired professor of theoretical physics in Sweden (affiliated with Uppsala University It then continues to describe Faddeev's contributions to automorphic functions, followed by an extensive account of his many fundamental contributions to field theory including his original article on ghosts with Popov.

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