arXiv subjects

Philip Turner

Publications and source records attributed to Philip Turner.

4 recordsLinked to original sources

arXiv2023

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost.

physics.chem-ph↗

arXiv2016

The physical principles underpinning self-organization in plants

Based on laboratory based growth of plant-like structures from inorganic materials, we present new theory for the emergence of plant structure at a range of scales dictated by levels of ionization (charge density), which can be traced directly back to proteins transcribed from genetic code and their interaction with external sources of charge (such as CO2) in real plants. Beyond a critical percolation threshold, individual charge induced quantum poten- tials (driven by dissipative systems) merge to form a complex, interconnected geometric web, creating macroscopic quantum potentials, which lead to the emergence of macroscopic quantum processes. The assembly of molecules into larger, ordered structures operates within these charge-induced coherent bosonic fields, acting as a structuring force in competition with exterior potentials. Within these processes many of the phenomena associated with standard quantum theory are recovered, including quantization, non-dissipation, self-organization, confinement, structuration conditioned by the environment, environmental fluctuations leading to macroscopic quantum decoherence and evolutionary time described by a time dependent Schrodinger-like equation, which describes models of bifurcation and duplication. The work provides a strong case for the existence of quintessence-like behaviour, with macroscopic quantum potentials and associated forces having their equivalence in standard quantum mechanics and gravitational forces in general relativity. The theory offers new insight into evolutionary processes in structural biology, with selection at any point in time, being made from a wide range of spontaneously emerging potential structures (dependent on conditions), which offer advantage for a specific organism. This is valid for both the emergence of structures from a prebiotic medium and the wide range of different plant structures we see today.

physics.gen-ph↗

arXiv2016

A new ab initio approach to the development of high temperature super conducting materials

We review recent theoretical developments, which suggest that a set of shared principles underpin macroscopic quantum phenomena observed in high temperature super conducting materials, room temperature coherence in photosynthetic processes and the emergence of long range order in biological structures. These systems are driven by dissipative systems, which lead to fractal assembly and a fractal network of charges (with associated quantum potentials) at the molecular scale. At critical levels of charge density and fractal dimension, individual quantum potentials merge to form a charged induced macroscopic quantum potential, which act as a structuring force dictating long range order. Whilst the system is only partially coherent (i.e. only the bosonic fields are coherent), within these processes many of the phenomena associated with standard quantum theory are recovered, with macroscopic quantum potentials and associated forces having their equivalence in standard quantum mechanics. We establish a testable hypothesis that the development of structures analogous to those found in biological systems, which exhibit macroscopic quantum properties, should lead to increased critical temperatures in high temperature superconducting materials. If the theory is confirmed it opens up a new, systematic, ab initio approach to the structural development of these types of materials.

physics.gen-ph↗

arXiv2015

The origins of macroscopic quantum coherence in high temperature super conductivity

A new, theoretical approach to macroscopic quantum coherence and superconductivity in the p-type (hole doped) cuprates is proposed. The theory includes mechanisms to account for e-pair coupling in the superconducting and pseudogap phases and their inter relations observed in these materials. Electron pair coupling in the superconducting phase is facilitated by local quantum potentials created by static dopants in a mechanism which explains experimentally observed optimal doping levels and the associated peak in critical temperature. By contrast, evidence suggests that electrons contributing to the pseudogap are predominantly coupled by fractal spin waves (fractons) induced by the fractal arrangement of dopants. On another level, the theory offers new insights into the emergence of a macroscopic quantum potential generated by a fractal distribution of dopants. This, in turn, leads to the emergence of coherent, macroscopic spin waves and a second associated macroscopic quantum potential, possibly supported by charge order. These quantum potentials play two key roles. The first involves the transition of an expected diffusive process (normally associated with Anderson localization) in fractal networks, into e-pair coherence. The second involves the facilitation of tunnelling between localized e-pairs. These combined effects lead to the merger of the super conducting and pseudo gap phases into a single coherent condensate at optimal doping. The underlying theory relating to the diffusion to quantum transition is supported by Coherent Random Lasing, which can be explained using an analogous approach. As a final step, an experimental program is outlined to validate the theory and suggests a new approach to increase the stability of electron pair condensates at higher temperatures.

cond-mat.supr-con↗