Parsimony as the ultimate regularizer for physics-informed machine learning

Nonlinear Dynamics - Data-driven modeling continues to be enabled by modern machine learning algorithms and deep learning architectures. The goals of such efforts revolve around the generation of...     

Towards the Antimicrobial Finishing of Poly(isoprene)

Summary: Anionically polymerised (poly)isoprene was functionalized with cysteamine applying thiol-ene click chemistry. Subsequent quaternisation of the primary amino groups gave polymers with antimicrobial activity against Listeria monocytogenes, Eschericchia coli, Pseudomonas fluorescens and Staphylococcus aureus as revealed from tests performed according to the Japanese Industrial Standard Z2801:2000. The novel polymers feature sufficient thermal stability for the compounding with commodity polymers such as poly(propylene) and might be used as a non leaching additive to finish commodity polymers with antimicrobial acitivity.     

Tuning the physisorption of molecular hydrogen: binding to aromatic,hetero-aromatic and metal-organic framework materials

We present a study on the binding properties of molecular hydrogen to several polar aromatic molecules and to a model for the metal-oxide corner of the metal organic framework materials recently investigated as promising supports for hydrogen storage. Density functional theory employing the Perdew Wang exchange-correlation functional and second order Møller-Plesset calculations are used to determine the equilibrium structures of complexes with molecular hydrogen and their stability. It is found that for most hetero-aromatics the edge sites for molecular hydrogen physisorption have stabilities comparable to the top sites. The DFT predicted binding energies compare favorably with those estimated at MP2 level, and get closer to the MP2 results for increased electrostatic contributions (induced by the polar aromatics) to the intermolecular interaction. Vibrational frequencies are also computed at the DFT level, and infrared activities of the H₂ stretching frequency are compared for the various complexes. Pyrrole, pyridine and n-oxide pyridine are predicted to form the more stable complexes among one-ring aromatics. The computed binding energies to metal-organic framework materials are in good agreement with experimental observations. It is suggested that replacement of the organic linker in MOF materials with some of the more efficient aromatics investigated here might contribute to enhance the H₂ storage properties of mixed inorganic–organic materials.     

An artificial pathway to 3,4-dihydroxybenzoic acid allows generation of new aminocoumarin antibiotic recognized by catechol transporters of E. coli

An artificial operon was synthesized, consisting of the genes for chorismate pyruvate-lyase of E. coli and for 4-hydroxybenzoate 3-hydroxylase of Corynebacterium cyclohexanicum. This operon, directing the biosynthesis of 3,4-dihdroxybenzoate, was expressed in the heterologous expression host Streptomyces coelicolor M512, together with a modified biosynthetic gene cluster for the aminocoumarin antibiotic clorobiocin. The resulting strain produced a clorobiocin derivative containing a 3,4-dihdroxybenzoyl moiety. Its structure was confirmed by MS and NMR analysis, and it was found to be a potent inhibitor of the gyrases from Escherichia coli and Staphylococcus aureus. Bioassays against different E. coli mutants suggested that this compound is actively imported by catechol siderophore transporters in the cell envelope. This study provides an example of the structure of a natural product that can be rationally modified by synthetic biology.     

The effect of n-, s- and t-butanol on the micellization and gelation of Pluronic P123 in aqueous solution

Thermodynamic and kinetics studies for adsorption of Pt ions complexes from the chloride solutions obtained by leaching chlorinated spent automotive catalysts on anionic exchange resin Diaion WA21J were carried out. It was found that only Si, Pt, Rh and Pd from the solution were selectively adsorbed on the resin Diaion WA21J more strongly. The adsorption equilibrium time for Pt ions was about 20 h. The isothermal adsorption of Pt ions was found to fit Langmuir, Freundlich and DKR models. The maximum monolayer adsorption capacities Q(max) and X(m) of Pt ions on the resin based on Langmuir and DKR model were 4.85, 5.36 and 5.69 mg/g as well as 5.01, 5.63 and 5.98 mg/g for temperatures 18°C, 28°C and 40°C, respectively. The apparent adsorption energy E(ad) based on DKR model were -11.79, -11.04 and -11.04 kJ/mol for the temperatures 18°C, 28°C and 40°C, respectively. Ion exchange was the mechanism involved in the adsorption process. The adsorption of Pt ions on the resin underwent pseudo-first-order kinetic process, and the apparent adsorption activation energy E(a,1) was 12.6 kJ/mol. The intraparticle diffusion of Pt ions was a main rate-controlling step in most of time of adsorption process.     

Polymorphism and isomerisation of an azobenzene derivative on gold

M-TBA (4-methoxy-3,30,5,50-tetra-tert-butylazobenzene) adsorbed on a gold (111) surface was found to form four different polymorphs, two of which isomerizable at -1.7 V, but with a low propensity for further isomerisation of nearby molecules (C. Dri, M. V. Peters, J. Schwarz, S. Hecht, L. Grill, Nat. Nanotechnol., 2008, 3, 649-653). Atomistic simulations investigate the origin of the effects.     

Intensity dynamics in a waveguide array laser

We consider experimentally and theoretically the optical field dynamics of a five-emitter laser array subject to a ramped injection current. We have achieved experimentally an array that produces a robust oscillatory power output with a nearly constant π phase shift between the oscillations from each waveguide. The output power also decreases linearly as a function of waveguide number. Those behaviors persisted for pump currents varying between 380 and 500 mA with only a slight change in phase. Of note is the fact that the fundamental frequency of oscillation increases with injection current, and higher harmonics are produced above a threshold current of approximately 380 mA. Experimental observations and theoretical predictions are in agreement. A low dimensional model was also developed and the impact of the nonuniform injection current studied. A nonuniform injection current is capable of shifting the bifurcations of the waveguide array providing a valuable method of array tuning without additional gain or structural alterations to the array.     

Communication: Vibrational spectroscopy of atmospherically relevant acid cluster anions: bisulfate versus nitrate core structures

Infrared multiple photon dissociation spectra for the smallest atmospherically relevant anions of sulfuric and nitric acid allow us to characterize structures and distinguish between clusters with a bisulfate or a nitrate core. We find that bisulfate is the main charge carrier for HSO(4)(-)·H(2)SO(4)·HNO(3) but not for NO(3)(-)·H(2)SO(4)·HNO(3). For the mixed dimer anion, we find evidence for the presence of two isomers: HSO(4)(-)·HNO(3) and NO(3)(-)·H(2)SO(4). Density functional calculations accompany the experimental results and provide support for these observations.     

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field.