arXiv subjects

Roland Riek

Publications and source records attributed to Roland Riek.

5 recordsLinked to original sources

arXiv2022

Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the major techniques in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size proteins in solution, living cells, and solids, but has been limited by the tedious data analysis process. It typically requires weeks or months of manual work of a trained expert to turn NMR measurements into a protein structure. Automation of this process is an open problem, formulated in the field over 30 years ago. Here, we present a solution to this challenge that enables the completely automated analysis of protein NMR data within hours after completing the measurements. Using only NMR spectra and the protein sequence as input, our machine learning-based method, ARTINA, delivers signal positions, resonance assignments, and structures strictly without any human intervention. Tested on a 100-protein benchmark comprising 1329 multidimensional NMR spectra, ARTINA demonstrated its ability to solve structures with 1.44 Å median RMSD to the PDB reference and to identify 91.36% correct NMR resonance assignments. ARTINA can be used by non-experts, reducing the effort for a protein assignment or structure determination by NMR essentially to the preparation of the sample and the spectra measurements.

q-bio.BM↗

arXiv2019

On the time continuous evolution of the universe if time is discrete and irreversible in nature

The time evolution of the universe is usually mathematically described under a continuous time and thus time reversible. Here, the consequences of studying the evolution of a homogenous isotropic universe by time continuous reversible physics are studied if time is actually discrete and irreversible in nature. The discrete dynamical time concept of Lee and its continuous time limit to the continuous time case is applied to the Newtonian limit of the general relativity theory. By doing so, the cosmic constant as well as the inflation of the universe arise and are predicted quantitatively well by assuming the smallest time step to be the Planck time and by using the current size of the universe.

physics.gen-ph↗

arXiv2019

On the nature of the Born rule

A physical experiment comprises along the time trajectory a start, a time evolution (duration), and an end, which is the measurement. In non relativistic quantum mechanics the start of the experiment is defined by the wave function at time 0 taking into account the starting conditions, the evolution is described by the wave function following the Schrödinger equation and the measurement by the Born rule. While the Schrödinger equation is deterministic, it is the Born rule that makes quantum mechanics statistical with all its consequences. The nature of the Born rule is thereby unknown albeit necessary since it produces the correct ensemble averaged measures of the experiment. Here, it is demonstrated that the origin of the Born rule is the projection from the quantum frame (i.e. wave description) to the classical mechanics frame (i.e. particle description) described by a Ehrenfest theorem-oriented Fourier transformation. The statistical averaging over many measurements is necessary in order to eliminate the unknown initial and end time coordinate of the experiment in reference to the beginning of the universe.

quant-ph↗

arXiv2016

On the Einstein-Podolsky-Rosen paradox using discrete time physics

The Einstein-Podolski-Rosen paradox highlights several strange properties of quantum mechanics including the super position of states, the non locality and its limitation to determine an experiment only statistically. Here, this well known paradox is revisited theoretically for a pair of spin 1/2 systems in a singlet state under the assumption that in classical physics time evolves in discrete time steps Deltat while in quantum mechanics the individual spin system(s) evolve(s) between the eigenstates harmonically with a period of 4 Deltat. It is further assumed that time is a single variable, that the quantum mechanics time evolution and the classical physics discrete time evolution are coherent to each other, and that the precision of the start of the experiment and of the measurement time point are much less than Deltat. Under these conditions, it is demonstrated for a spin 1/2 system that the fast oscillation between the eigen states spin up and spin down reproduces the expected outcome of a single measurement as well as ensemble measurements without the need of postulating a simultaneous superposition of the spin system in its quantum state. When this concept is applied to a spin 1/2 system pair in a singlet state it is shown that no entanglement between the two spins is necessary to describe the system resolving the Einstein-Podolski-Rosen paradox.

quant-ph↗

arXiv2014

A derivation of a microscopic entropy and time irreversibility from the discreteness of time

All of the basic microsopic physical laws are time reversible. In contrast, the second law of thermodynamics, which is a macroscopic physical representation of the world, is able to describe irreversible processes in an isolated system through the change of entropy S larger than 0. It is the attempt of the present manuscript to bridge the microscopic physical world with its macrosocpic one with an alternative approach than the statistical mechanics theory of Gibbs and Boltzmann. It is proposed that time is discrete with constant step size. Its consequence is the presence of time irreversibility at the microscopic level if the present force is of complex nature (i.e. not const). In order to compare this discrete time irreversible mechamics (for simplicity a classical, single particle in a one dimensional space is selected) with its classical Newton analog, time reversibility is reintroduced by scaling the time steps for any given time step n by the variable sn leading to the Nose-Hoover Lagrangian. The corresponding Nose-Hoover Hamiltonian comprises a term Ndf *kB*T*ln(sn) (with kB the Boltzmann constant, T the temperature, and Ndf the number of degrees of freedom) which is defined as the microscopic entropy Sn at time point n multiplied by T. Upon ensemble averaging this microscopic entropy Sn in equilibrium for a system which does not have fast changing forces approximates its macroscopic counterpart known from thermodynamics. The presented derivation with the resulting analogy between the ensemble averaged microscopic entropy and its thermodynamic analog suggests that the original description of the entropy by Boltzmann and Gibbs is just an ensemble averaging of the time scaling variable sn which is in equilibrium close to 1, but that the entropy term itself has its root not in statistical mechanics but rather in the discreteness of time.

physics.chem-ph↗