Monte Carlo simulations reveal the straightening up of an end-grafted flexible chain with a rigid side chain

We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we observe a considerable straightening of the flexible backbone as quantified via the gyration tensor. For $b=N$, i.e. when attaching the side chain to the free end of the flexible backbone, the effect was strongest

Anomalous Diffusion and Non-classical Reaction Kinetics in Crowded Fluids

This thesis investigates the underlying mechanism and the effects of anomalous diffusion in crowded fluids by means of computer simulations. In order to elucidate the mechanism behind crowding-induced subdiffusion we discuss the average shape of tracer trajectories as a potential criterion that allows to reliably discriminate between frequently proposed models. Our simulations show that measurement errors inherent to single particle tracking generally impair the determination of the underlying random process from experimental data. We propose a particle-based model for the crowded cytoplasm that incorporates soft-core repulsion and weak attraction between globular proteins of various sizes. Under these prerequisites simulations reveal transient subdiffusion of proteins. On experimental time scales, however, diffusion is normal indicating that realistic, microscopic models of crowded fluids require further detail of the relevant interactions. In the second part of this thesis, the impact of subdiffusion on biochemical reactions is studied via mesoscopic, stochastic simulations. Due to their compact trajectories subdiffusive reactants get increasingly segregated over time. This results in anomalous kinetics that differs strongly from classical theories. Moreover, for a two-step reaction scheme relying on an intermediate dissociation-association event, subdiffusion can substantially improve the overall productivity because spatio-temporal correlations are exploited with high efficiency

Functional Nanopores: A Solid-state Concept for Artificial Reaction Compartments and Molecular Factories

On the road towards the long-term goal of the NCCR Molecular Systems Engineering to create artificial molecular factories, we aim at introducing a compartmentalization strategy based on solid-state silicon technology targeting zeptoliter reaction volumes and simultaneous electrical contact to ensembles of well-oriented molecules. This approach allows the probing of molecular building blocks under a controlled environment prior to their use in a complex molecular factory. Furthermore, these ultra-sensitive electrical conductance measurements allow molecular responses to a variety of external triggers to be used as sensing and feedback mechanisms. So far, we demonstrate the proof-of-concept by electrically contacting self-assembled mono-layers of alkane-dithiols as an established test system. Here, the molecular films are laterally constrained by a circular dielectric confinement, forming a so-called `nanopore`. Device yields above 85% are consistently achieved down to sub-50 nm nanopore diameters. This generic platform will be extended to create distributed, cascaded reactors with individually addressable reaction sites, including interconnecting micro-fluidic channels for electrochemical communication among nanopores and sensing sites for reaction control and feedback. In this scientific outlook, we will sketch how such a solid-state nanopore concept can be used to study various aspects of molecular compounds tailored for operation in a molecular factory

Electrochemical Multiplexing: Control over Surface Functionalization by Combining a Redox-Sensitive Alkyne Protection Group with "Click"-Chemistry

Local functionalization of surfaces is a current technological challenge. An electrochemically addressable alkyne protection group is presented enabling the site-selective liberation of alkynes exclusively on electrified electrodes. This controlled deprotection is based on a mendione chromophore which becomes a strong enough nucleophile upon reduction to intramolecularly attack the trialkylsilane alkyne protection group. The site-selective liberation of the alkyne is demonstrated by immobilizing the protected alkyne precursor on a transparent TiO2 electrode and subsequently immobilizing red and blue azide dyes by azide-alkyne "click"-chemistry. While the proof-of-principle is based on colorations visible to the bare eye, the technique presented is generic also to nontransparent electrodes, microscale separations, and functional moieties other than dyes. It may open manifold applications where site-selective functionalization is required but hardly realizable with conventional methods

protocol of a prospective, longitudinal study

Background Natural killer (NK) cells comprise the main components of lymphocyte-mediated nonspecific immunity. Through their effector function they play a crucial role combating bacterial and viral challenges. They are also thought to be key contributors to the systemic spinal cord injury-induced immune-deficiency syndrome (SCI-IDS). SCI-IDS increases susceptibility to infection and extends to the post-acute and chronic phases after SCI. Methods and design The prospective study of NK cell function after traumatic SCI was carried out in two centers in Berlin, Germany. SCI patients and control patients with neurologically silent vertebral fracture also undergoing surgical stabilization were enrolled. Furthermore healthy controls were included to provide reference data. The NK cell function was assessed at 7 (5–9) days, 14 days (11–28) days, and 10 (8–12) weeks post-trauma. Clinical documentation included the American Spinal Injury Association (ASIA) impairment scale (AIS), neurological level of injury, infection status, concomitant injury, and medications. The primary endpoint of the study is CD107a expression by NK cells (cytotoxicity marker) 8–12 weeks following SCI. Secondary endpoints are the NK cell’s TNF-α and IFN-γ production by the NK cells 8–12 weeks following SCI. Discussion The protocol of this study was developed to investigate the hypotheses whether i) SCI impairs NK cell function throughout the post-acute and sub-acute phases after SCI and ii) the degree of impairment relates to lesion height and severity. A deeper understanding of the SCI-IDS is crucial to enable strategies for prevention of infections, which are associated with poor neurological outcome and elevated mortality. Trial registration DRKS00009855

The spinal cord injury-induced immune deficiency syndrome: results of the SCIentinel study

Infections are prevalent after spinal cord injury (SCI), constitute the main cause of death and are a rehabilitation confounder associated with impaired recovery. We hypothesize that SCI causes an acquired lesion-dependent (neurogenic) immune suppression as an underlying mechanism to facilitate infections. The international prospective multicentre cohort study (SCIentinel; protocol registration DRKS00000122; n = 111 patients) was designed to distinguish neurogenic from general trauma-related effects on the immune system. Therefore, SCI patient groups differing by neurological level, i.e. high SCI [thoracic (Th)4 or higher]; low SCI (Th5 or lower) and severity (complete SCI; incomplete SCI), were compared with a reference group of vertebral fracture (VF) patients without SCI. The primary outcome was quantitative monocytic Human Leukocyte Antigen-DR expression (mHLA-DR, synonym MHC II), a validated marker for immune suppression in critically ill patients associated with infection susceptibility. mHLA-DR was assessed from Day 1 to 10 weeks after injury by applying standardized flow cytometry procedures. Secondary outcomes were leucocyte subpopulation counts, serum immunoglobulin levels and clinically defined infections. Linear mixed models with multiple imputation were applied to evaluate group differences of logarithmic-transformed parameters. Mean quantitative mHLA-DR [ln (antibodies/cell)] levels at the primary end point 84 h after injury indicated an immune suppressive state below the normative values of 9.62 in all groups, which further differed in its dimension by neurological level: high SCI [8.95 (98.3% confidence interval, CI: 8.63; 9.26), n = 41], low SCI [9.05 (98.3% CI: 8.73; 9.36), n = 29], and VF without SCI [9.25 (98.3% CI: 8.97; 9.53), n = 41, P = 0.003]. Post hoc analysis accounting for SCI severity revealed the strongest mHLA-DR decrease [8.79 (95% CI: 8.50; 9.08)] in the complete, high SCI group, further demonstrating delayed mHLA-DR recovery [9.08 (95% CI: 8.82; 9.38)] and showing a difference from the VF controls of -0.43 (95% CI: -0.66; -0.20) at 14 days. Complete, high SCI patients also revealed constantly lower serum immunoglobulin G [-0.27 (95% CI: -0.45; -0.10)] and immunoglobulin A [-0.25 (95% CI: -0.49; -0.01)] levels [ln (g/l × 1000)] up to 10 weeks after injury. Low mHLA-DR levels in the range of borderline immunoparalysis (below 9.21) were positively associated with the occurrence and earlier onset of infections, which is consistent with results from studies on stroke or major surgery. Spinal cord injured patients can acquire a secondary, neurogenic immune deficiency syndrome characterized by reduced mHLA-DR expression and relative hypogammaglobulinaemia (combined cellular and humoral immune deficiency). mHLA-DR expression provides a basis to stratify infection-risk in patients with SCI