In this paper, a novel discrete algebra is presented which follows by combining the SU(2) Lie-Poisson bracket with the discrete Frenet equation. Physically, the construction describes a discrete piecewise linear string in R³. The starting point of our derivation is the discrete Frenet frame assigned at each vertex of the string. Then the link vector that connects the neighboring vertices is assigned the SU(2) Lie-Poisson bracket. Moreover, the same bracket defines the transfer matrices of the discrete Frenet equation which relates two neighboring frames along the string. The procedure extends in a self-similar manner to an infinite hierarchy of Poisson structures. As an example, the first descendant of the SU(2) Lie-Poisson structure is presented in detail. For this, the spinor representation of the discrete Frenet equation is employed, as it converts the brackets into a computationally more manageable form. The final result is a nonlinear, nontrivial, and novel Poisson structure that engages four neighboring vertices.

We show that topology is a very effective tool, to construct classical Hamiltonian time crystals. For this we numerically analyze a general class of time crystalline Hamiltonians that are designed to model the dynamics of molecular closed strings. We demonstrate how the time crystalline qualities of a closed string are greatly enhanced when the string becomes knotted. The Hamiltonians that we investigate include a generalized Kratky-Porod wormlike chain model in combination with long range Coulomb and Lennard-Jones interactions. Such energy functions are commonplace in coarse grained molecular modeling. Thus we expect that physical realizations of Hamiltonian time crystals can be constructed in terms of knotted ring molecules.

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 phenomenon is presented. For this the thermal vibrations of individual atoms in an isolated cyclopropane molecule are simulated in vacuum and at ultra-low internal temperature values. When the molecule is observed stroboscopically, at discrete equidistant time steps, the random thermal vibrations of the individual atoms become self-organized into a collective oscillatory motion of the entire molecule. The period of oscillation is emergent and intrinsic to the molecule so that this self-organization bears resemblance to a driven time crystal. The oscillation period increases in a self-similar manner when the length of the stroboscopic time step is increased. In the limit of very long stroboscopic time steps the entire molecule can then rotate in an apparent uniform fashion, but with no angular momentum. It is proposed that the observed behavior is universal in the case of triangular molecules. Moreover, it is shown that the emergent uniform rotation without any angular momentum, can be described in an effective theory approach as an autonomous Hamiltonian time crystal. The emergent oscillatory motion appears to be highly sensitive to temperature. This proposes that potential applications could be found from the development of molecular level detector to sensor and control technologies.

Vortices in a Bose-Einstein condensate are modelled as spontaneously symmetry breaking minimum energy solutions of the time dependent Gross-Pitaevskii equation, using the method of constrained optimization. In a non-rotating axially symmetric trap, the core of a single vortex precesses around the trap center and, at the same time, the phase of its wave function shifts at a constant rate. The precession velocity, the speed of phase shift, and the distance between the vortex core and the trap center, depend continuously on the value of the conserved angular momentum that is carried by the entire condensate. In the case of a symmetric pair of identical vortices, the precession engages an emergent gauge field in their relative coordinate, with a flux that is equal to the ratio between the precession and shift velocities.

Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone C(alpha)chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.

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 spontaneously broken by a time crystal, that we define as the minimum of the available mechanical free energy that is simultaneously a time dependent solution of Hamilton's equation. The mathematical description of such a timecrystalline spontaneous symmetry breaking builds on concepts of equivariant Morse theory in the space of Hamiltonian flows. As an example we analyze a general family of timecrystalline Hamiltonians that is designed to model polygonal, piecewise linear closed strings. The vertices correspond to the locations of pointlike interaction centers; the string is akin a chain of atoms, that are joined together by covalent bonds, modeled by the links of the string. We argue that the timecrystalline character of the string can be affected by its topology. For this we show that a knotty string is usually more timecrystalline than a string with no self-entanglement. We also reveal a relation between phase space topology and the occurrence of timecrystalline dynamics. For this we show that in the case of three point particles, the presence of a time crystal can relate to a Dirac monopole that resides in the phase space. Our results propose that physical examples of Hamiltonian time crystals can be realized in terms of closed, knotted molecular rings.

Classical Hamiltonian systems with conserved charges and those with constraints often describe dynamics on a pre-symplectic manifold. Here we show that a pre-symplectic manifold is also the proper stage to describe autonomous energy conserving Hamiltonian time crystals. We explain how the occurrence of a time crystal relates to the wider concept of spontaneously broken symmetries; in the case of a time crystal, the symmetry breaking takes place in a dynamical context. We then analyze in detail two examples of timecrystalline Hamiltonian dynamics. The first example is a piecewise linear closed string, with dynamics determined by a Lie-Poisson bracket and Hamiltonian that relates to membrane stability. We explain how the Lie-Poisson brackets descents to a time-crystalline pre-symplectic bracket, and we show that the Hamiltonian dynamics supports two phases; in one phase we have a time crystal and in the other phase time crystals are absent. The second example is a discrete one dimensional model of a Hamiltonian chain. It is obtained by a reduction from the Q-ball Lagrangian that describes time dependent nontopological solitons. We show that a time crystal appears as a minimum energy domain wall configuration, along the chain.

We inquire to what extent can the geometry of protein peptide plane and side chain atoms be reconstructed from the knowledge of C time evolution. Due to the lack of experimental data, we analyze all atom molecular dynamics trajectories from the Anton supercomputer, and for clarity, we limit our attention to the peptide plane O atoms and side chain C atoms. We reconstruct their positions using four different approaches. Three of these are the publicly available reconstruction programs Pulchra, Remo, and Scwrl4. The fourth, Statistical Method, builds entirely on the statistical analysis of Protein Data Bank structures. All four methods place the O and C atoms accurately along the Anton trajectories; the Statistical Method gives results that are closest to the Anton data. The results suggest that when a protein moves under physiological conditions, its all atom structures can be reconstructed with high accuracy from the knowledge of the C atom positions. This can help to better understand and improve all atom force fields, and advance reconstruction and refinement methods for reduced protein structures. The results provide impetus for the development of effective coarse grained force fields in terms of reduced coordinates.

The shape of a protein can be modeled by the C atoms of its backbone, the mathematical description employing the notion of extrinsic geometry of a discrete piecewise linear chain. We advance differential geometry of a natively framed discrete chain to argue the existence of two additional, independent and intrinsic geometric structures, provided by the peptide planes and side chains, respectively. We develop our general methodology within a case study: analysis of the intrinsic geometry of atoms that are located around a non-proline cis peptide plane. We show that the native peptide plane framing allows for revealing of atomic positions anomalies. That way, we identify a number of entries that display such anomalies around their non-proline cis peptide planes within the ultrahigh-resolution structures in PDB. We propose that our approach can be extended into a visual analysis and refinement tool that is applicable even when resolution is limited or data is incomplete, for example when there are atoms missing in an experimental construct.

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. The effective Hamiltonian involves unusual Poisson brackets that bring in noncommutative geometry. In idealized models of ring molecules, we find time crystal behavior is widespread.