Search results for "Biomolecule"
showing 10 items of 666 documents
Effect of opsin on the shape of the potential energy surfaces at the conical intersection of the Rhodopsin chromophore
2008
Abstract In order to disentangle the role of the protein in the control of the photoisomerization of the chromophore of the visual pigment Rhodopsin, we compare the structure of the ground and excited potential energy surfaces of gas-phase and opsin-embedded 11- cis retinal chromophore at the corresponding (lowest energy) conical intersections. It is shown that, along the branching plane, the asymmetric opsin environment destabilizes one of the ground state relaxation channels emerging from the conical intersection. This suggests that opsin promotes the formation of the product (bathorhodopsin) via enhanced decay probability along the all- trans exit channel. In contrast, in the gas-phase n…
"Table 2" of "Measurement of the correlations between the polar angles of leptons from top quark decays in the helicity basis at $\sqrt{s}=7$TeV usin…
2017
The correlation factors for the statistical uncertainties between any two bins of the unfolded distribution.
What is the order of the two-dimensional polymer escape transition?
2007
An end-grafted flexible polymer chain in three-dimensional space between two pistons undergoes an abrupt transition from a confined coil to a flowerlike conformation when the number of monomers in the chain, $N$, reaches a critical value. In two-dimensional (2D) geometry, excluded-volume interactions between monomers of a chain confined inside a strip of finite length $2L$ transform the coil conformation into a linear string of blobs. However, the blob picture raises questions about the nature of this escape transition. To check theoretical predictions based on the blob picture we study 2D single-polymer chains with excluded-volume interactions and with one end grafted in the middle of a st…
Coarse Graining of Short Polythylene Chains for Studying Polymer Crystallization.
2015
We derive coarse-grained models of polyethylene in the melt state with the aim to study polymer crystallization. This requires a low level of coarse-graining: We use a mapping of two CH2 groups onto one bead. The coarse-grained beads are connected with harmonic springs, an optimized angular potential, and an optional torsional potential. Coarse-grained potentials are derived from detailed all-atom simulations, and an optimized form of the force field is then derived which achieves a good accuracy in reproducing the static properties of the chains. We address the question over which temperature range such models can be used, and in particular if the model is capable of reproducing the phase…
Simulation of Phase Transitions of Single Polymer Chains: Recent Advances
2006
The behaviour of a flexible polymer chain in solvents of variable quality in dilute solution is discussed both in the bulk and in the presence of an adsorbing wall. Monte Carlo simulations of coarse-grained bead-spring models and of the bond fluctuation model are presented and interpreted in terms of phenomenological theories and scaling concepts. Particular attention is paid to the behaviour of the polymer chain when the temperature of the polymer solution gets lower than the Theta temperature. It is argued that the adsorption transition line at the Theta temperature splits into lines of wetting and drying transitions of polymer globules attached to the wall. In addition, it is shown that …
Ferrochirality: a simple theoretical model of interacting, dynamically invertible, helical polymers, 2. Molecular field approach: supports and the de…
1995
Using a molecular field approach, the effect of interaction between reversibly invertible, helical polymers is investigated theoretically. The helices are modelled by nearest-neighbour statistical thermodynamics. If the interaction energy between two helices of common handedness is lower than that of oppositely handed ones, a critical temperature Tc exists, below which the system spontaneously must leave the racemic state, though there is no contact to any chiral centre or force. This is analogous to the second-order phase transition of ferromagnets. The critical point increases with molecular weight and optical persistence of the helices. At the critical point the system is highly sensitiv…
Communication: Protein dynamical transition vs. liquid-liquid phase transition in protein hydration water
2013
In this work, we compare experimental data on myoglobin hydrated powders from elastic neutron scattering, broadband dielectric spectroscopy, and differential scanning calorimetry. Our aim is to obtain new insights on the connection between the protein dynamical transition, a fundamental phenomenon observed in proteins whose physical origin is highly debated, and the liquid-liquid phase transition (LLPT) possibly occurring in protein hydration water and related to the existence of a low temperature critical point in supercooled water. Our results provide a consistent thermodynamic/dynamic description which gives experimental support to the LLPT hypothesis and further reveals how fundamental …
Molecular Basis of DNA Photodimerization: Intrinsic Production of Cyclobutane Cytosine Dimers
2008
Based on CASPT2 results, the present contribution establishes for the first time that cytosine photodimer formation (CC) is mediated along the triplet and singlet manifold by a singlet-triplet crossing, (T1/S0)X, and by a conical intersection, (S1/S0)CI, respectively. The former can be accessed in a barrierless way from a great variety of photochemical avenues and exhibits a covalent single bond between the ethene C6-C6' carbon atoms of each monomer. The efficiency of the stepwise triplet mechanism, however, would be modulated by the effectiveness of the intersystem crossing mechanism. The results provide the grounds for the understanding of the potential photogenotoxicity of endogenous and…
Theoretical study of excitation transfer from modified B800 rings of the LH II antenna complex of Rps. acidophila
2002
The recently developed configuration interaction exciton model has been applied to study spectral shifts and B800 to B850 energy transfer rates in a series of modified LH2 light harvesting antenna complexes of the purple bacterium Rhodopseudomonas acidophila. Complexes, where the in vivo B800 bacteriochlorophyll a chromophores are exchanged with different tetrapyrroles including chlorophyll a were studied. Absorption spectra of the modified complexes were simulated by using quantum chemical methods to evaluate site and interaction energies and exciton theory to generate the eigenstates of the chromophore assemblies. Four experimental input parameters: the transition moment of Bchl a, the di…
Alkoxy-styryl DCDHF fluorophores
2010
A photostable dicyanomethylenedihydrofuran fluorophore which contains electron-donating alkoxy groups is described. This chromophore is highly environmentally-sensitive, which is a remarkable property for a fluorescent reporter. Its light excitation also enables, in low viscous solvents, the formation of dark states whose radical or triplet nature is ruled out.