Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins

Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress relaxation in hydrated lysozyme proteins stimulated and probed by X-ray Photon Correlation Spectroscopy (XPCS). This approach allows us to access the nanoscale dynamic response in the deeply supercooled regime (T = 180 K) which is typically not accessible through equilibrium methods. The relaxation time constants exhibit Arrhenius temperature dependence upon cooling with a minimum in the Kohlrausch-Williams-Watts exponent at T = 227 K. The observed minimum is attributed to an increase in dynamical heterogeneity, which coincides with enhanced fluctuations observed in the two-time correlation functions and a maximum in the dynamic susceptibility quantified by the normalised variance $\chi_T$. Our study provides new insights into X-ray stimulated stress relaxation and the underlying mechanisms behind spatio-temporal fluctuations in biological granular materials

Development of a water model with arbitrary rank multipolar polarization, repulsion and electrostatics

I report on the derivation, development and computer implementation of methods for computing the energies and forces between small rigid polarizable molecules, that are defined by the center-of-mass moments of their electronic and nuclear charge distributions and their linear response moments. The formalism is based on compact and efficient storage and manipulation of symmetric Cartesian tensors of arbitrary rank, and a general formula for the Cartesian gradients of one-dimensional interaction (kernel) potentials. The theory is applied to many-body interactions among water molecules. Permanent moments of the water molecule are computed up to the 9th order with quantum-chemistry software and their basis-set dependence is investigated. Response moments up to the 5th order are similarly investigated. Kernel potentials for electronic, nuclear and polarized interactions are suggested and compared to interaction energies from symmetry-adapted perturbation-theory. I discuss vibrational degrees of freedom and report on a novel method for fitting high rank moment tensors to a flexible geometry. The method is based on decomposition of the tensor into a sum of outer products of vectors, which are defined in the lab-frame by the molecular geometry. I show that the formalism, which is based on an asymptotic expansion, can give good results at all ranges.

Hastighetskonstanten för Strålningsassociation av CF⁺

Validerat; 20150930 (global_studentproject_submitter

A flexible and polarizable water model built on interpolated multipoles

Water has a rich phase diagram with regions of meta-stability, the prime examples being super-cooled and super-heated liquid water.Below ca 50 °C, water exhibits unusual and not yet fully explained anomalous thermodynamic properties upon cooling, for example a minimum in compressibility at 46 °C, a minimum in heat capacity at 35 °C, a density maximum at 4 °C, and a compressibility maximum at -44 °C in the supercooled liquid, at ambient pressure.It is hypothesized that the phase transition (PT) between high- and low-density amorphous ices, below ~120 K, extends toward ambient conditions as a PT between two liquid phases, and ends at a critical point in the deeply supercooled liquid, giving rise to critical fluctuations in density that explain the anomalies.The phase diagram can be examined with molecular dynamics (MD) simulations, where the molecular structure is a direct observable.The realism of a simulation improves with the accuracy of model forces, the number of molecules, and simulated time.Accurate forces can be obtained from wave function (WF) calculations, but the computational demands are high.In computationally efficient models, the accuracy is generally compromised,but with the advent of machine learning, this situation has improved. In this thesis we report on the development of a water model that aims for accuracy similar to the best WF methods, while being efficient enough for predictive MD simulations.Multipole and polarizability tensors have been computed with WF methods for a training set of perturbed water monomers, and fitted with Gaussian process regression as functions of the molecular geometry, in order to create an accurate model of the electrostatic and many-body polarization forces.To obtain accurate short-range forces, due to intermolecular WF overlap, a machine-learning (Gaussian approximation) potential is applied, which is trained on the difference (in forces and energies) between the electrostatic model and an accurate WF method, for a large training-set of water dimers and trimers.To facilitate periodic calculations at constant pressure, the Ewald method and virial stress tensor have been implemented for multipolar forces between flexible molecules.The model shows good agreement with WF calculations of the energies of different test-structures, as well as promising results for thermodynamic properties from MD simulations

Development of a water model with arbitrary rank multipolar polarization, repulsion and electrostatics

I report on the derivation, development and computer implementation of methods for computing the energies and forces between small rigid polarizable molecules, that are defined by the center-of-mass moments of their electronic and nuclear charge distributions and their linear response moments. The formalism is based on compact and efficient storage and manipulation of symmetric Cartesian tensors of arbitrary rank, and a general formula for the Cartesian gradients of one-dimensional interaction (kernel) potentials. The theory is applied to many-body interactions among water molecules. Permanent moments of the water molecule are computed up to the 9th order with quantum-chemistry software and their basis-set dependence is investigated. Response moments up to the 5th order are similarly investigated. Kernel potentials for electronic, nuclear and polarized interactions are suggested and compared to interaction energies from symmetry-adapted perturbation-theory. I discuss vibrational degrees of freedom and report on a novel method for fitting high rank moment tensors to a flexible geometry. The method is based on decomposition of the tensor into a sum of outer products of vectors, which are defined in the lab-frame by the molecular geometry. I show that the formalism, which is based on an asymptotic expansion, can give good results at all ranges.