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Calculating binding free energies with quan-tum-mechanical (QM) methods is notoriously time-consum-ing. In this work, we studied whether such calculations can beaccelerated by using nonequilibrium (NE) moleculardynamics simulations employing Jarzynski’s equality. Westudied the binding of nine cyclic carboxylate ligands to theocta-acid deep-cavity host from the SAMPL4 challenge withthe reference po
The enzyme nitrogenase contains a complicated MoFe7CS9 cofactor with 35 possible broken- symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one- electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Lik
We have devised a new efficient approach tocompute combined quantum mechanical (QM) and molecularmechanical (MM, i.e. QM/MM) ligand-binding relative freeenergies. Our method employs the reference-potentialapproach with free-energy perturbation both at the MMlevel (between the two ligands) and from MM to QM/MM(for each ligand). To ensure that converged results areobtained for the MM → QM/MM perturb
Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal struc- tures. Due to this natural synergy, nowadays accurate distri- butions of electrons in space can be obtained from diffrac- tion and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huan
Background Little is known about factors contributing to the altered movement patterns observed in many individuals with anterior cruciate ligament (ACL) injury. We addressed whether altered muscular activity is such a factor. Methods 16 participants with unilateral, non-reconstructed ACL rupture were scored for altered movement patterns according to Test for Substitution Patterns (TSP), which inc
Background: Faculty development roles are changing within organizations (Gibbs 2013). In previous research the expanding role in organizations as “Coming in from the margins” was described (Schroeder 2011). We studied how different levels of participation evolved within a research intense faculty with a complex organization and various educational programs.Summary of Work: The Centre was establish
Projectile Coulomb excitation experiments were performed at HIE-ISOLDE at CERN with the radioactive ion beams of 140Nd and 142Sm. Ions with an energy of 4:62 MeV/A were impinging on a 1.45 mg/cm2 thick 208Pb target. The γ-rays depopulating the Coulomb-excited states were recorded by the HPGe-array MINIBALL and scattered particles were detected by a double-sided silicon strip detector. Experimental
Dysfunctional insulin secretion is a hallmark of type 2 diabetes (T2D). Interestingly, several islet microRNAs (miRNAs) are upregulated in T2D, including miR-132. We aimed to investigate whether in vivo treatment with antagomir-132 lowers expression of miR-132 in islets thereby improving insulin secretion and lowering blood glucose. Mice injected with antagomir-132 for 24 h, had reduced expression
Tack vare ett näst intill oändligt antal variationer så har proteiner blivit naturens standardlösning för diverse uppgifter och problem. I våra egna kroppar har vi en uppsjö av olika varianter där några är allmänt välkända, t.ex. hemoglobin i våra röda blodkroppar som transporterar runt syre och insulin vilket sänker vår blodsockernivå. Andra proteiner är mer okända men trots det lika viktiga, exeThe behavior of concentrated protein solutions is of general high interest due to implications in, for example, biological systems and medical applications. It is necessary to investigate the rheological properties of such systems to understand how parameters, such as stability, are affected by the high concentrations. Unfortunately, studies are often hindered by the lack of sufficient quantities
It is well known that marine fish dynamics relate with climate variability, and predicting future population developments have become increasingly urgent with on-going climate change. One approach in widespread populations is to study how individuals from different parts of the distribution area respond to climate, thereby testing for potential resilience in terms of local adaptions against enviro
