CCharPPI web server: computational characterization of protein–protein interactions from structure

The atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework Programme (FP7/2007- 2013) under REA grant agreement PIEF-GA-2012-327899 and grant BIO2013-48213-R from Spanish Ministry of Economy and Competitiveness.Peer ReviewedPostprint (published version

Modelling of submerged membrane bioreactor: Conceptual study about link between activated slugde biokinetics, aeration and fouling process

A mathematical model was developed to simulate filtration process and aeration influence on Submerged Membrane Bioreactor (SMBR) in aerobic conditions. The biological kinetics and the dynamic effect of the sludge attachment and detachment from the membrane, in relation to the filtration and a strong intermittent aeration, were included in the model. The model was established considering soluble microbial products (SMP) formation-degradation. The fouling components responsible of pore clogging, sludge cake growth, and temporal sludge film coverage were considered during calculation of the total membrane fouling resistance. The influence of SMP, trans-membrane pressure, and mixed liquor suspended solids on specific filtration resistance of the sludge cake was also included. With this model, the membrane fouling under different SMBR operational conditions can be simulated. The influence of a larger number of very important process variables on fouling development can be well quantified. The model was developed for evaluating the influence on fouling control of an intermittent aeration of bubbles synchronized or not with the filtration cycles, taking into account the effects of shear intensity on sludge cake removal

Detecting and Estimating Signals in Noisy Cable Structures, I: Neuronal Noise Sources

In recent theoretical approaches addressing the problem of neural coding, tools from statistical estimation and information theory have been applied to quantify the ability of neurons to transmit information through their spike outputs. These techniques, though fairly general, ignore the specific nature of neuronal processing in terms of its known biophysical properties. However, a systematic study of processing at various stages in a biophysically faithful model of a single neuron can identify the role of each stage in information transfer. Toward this end, we carry out a theoretical analysis of the information loss of a synaptic signal propagating along a linear, one-dimensional, weakly active cable due to neuronal noise sources along the way, using both a signal reconstruction and a signal detection paradigm. Here we begin such an analysis by quantitatively characterizing three sources of membrane noise: (1) thermal noise due to the passive membrane resistance, (2) noise due to stochastic openings and closings of voltage-gated membrane channels (Na^+ and K^+), and (3) noise due to random, background synaptic activity. Using analytical expressions for the power spectral densities of these noise sources, we compare their magnitudes in the case of a patch of membrane from a cortical pyramidal cell and explore their dependence on different biophysical parameters

Constraints on the variability of quark masses from nuclear binding

Based on recent work on nuclear binding, we update and extend the anthropic constraints on the light quark masses, with results that are more tightly constrained than previously obtained. We find that heavy nuclei would fall apart (because the attractive nuclear central potential becomes too weak) if the sum of the light quark masses m_u+m_d would exceed their physical values by 64% (at 95% confidence level). We summarize the anthropic constraints that follow from requiring the existence both of heavy atoms and of hydrogen. With the additional assumption that the quark Yukawa couplings do not vary, these constraints provide a remarkably tight anthropic window for the Higgs vacuum expectation value: 0.39 < v/v_physical < 1.64.Comment: 21 pages, 7 figure

A mathematical model of Doxorubicin treatment efficacy on non-Hodgkin’s lymphoma: Investigation of current protocol through theoretical modelling results

Doxorubicin treatment outcomes for non-Hodgkin’s lymphomas (NHL) are mathematically modelled and computationally analyzed. The NHL model includes a tumor structure incorporating mature and immature vessels, vascular structural adaptation and NHL cell-cycle kinetics in addition to Doxorubicin pharmacokinetics (PK) and pharmacodynamics (PD). Simulations provide qualitative estimations of the effect of Doxorubicin on high-grade (HG), intermediate-grade (IG) and low-grade (LG) NHL. Simulation results imply that if the interval between successive drug applications is prolonged beyond a certain point, treatment will be inefficient due to effects caused by heterogeneous blood flow in the system