International Business Machines Corporation

Globalfoundries Inc.

Columbia University

Zhejiang University

Ruhong Zhou

Binquan Luan

Ajay K Royyuru

Benjamin David Silverman

Prasanna Athma

Bruce J Berne

Clifford A Pickover

James R Kozloski

Laxmi Priya Parida

Guojing Cong

Giacomo Domeniconi

Chih-Chieh Yang

Leili Zhang

Edward Harder

Huafeng Xu

Jacinta M Wubben

Lianxue Zhang

A computer-implemented method for executing a computation task in a molecular dynamic simulation includes identifying a bonding target on a ligand; constructing a protein structure; rendering an image of the ligand; subsampling data pertaining to the constructed protein structure and the image of the ligand at a particular frequency; rendering a two-dimensional image of the constructed protein structure relative to the ligand from a plurality of viewpoints; computing optical flows of the protein structure relative to the ligand based on the two-dimensional image; analyzing the optical flows to determine a displacement of atoms; simulating a binding state outcome of the protein structure relative to the ligand for each of the plurality of viewpoints; and predicting a probability of the protein structure binding with the ligand, based on the predicted binding state outcome for each of the plurality of viewpoints.

Optical flow based forecasting of binding states in molecular dynamic simulations

A high-efficiency anti-tumor nano-drug delivery system containing hydralazine (hydralazine-nanoparticles abbreviated as H-NPs) is provided. The drug delivery system takes hydralazine and doxorubicin combined by a &#x3c0;-&#x3c0; bond as a hydrophobic core and takes dextran as a hydrophilic shell. The high-effective anti-tumor nano-drug delivery system containing hydralazine can increase the vascular permeability and blood perfusion of the tumor site, improve the enrichment and penetration of nanoparticles in the tumor, reduce tumor hypoxia, increase the sensitivity of the tumor to a chemotherapy drug doxorubicin, and significantly improve its anti-tumor effect by expanding the tumor blood vessels and regulating tumor microenvironment (TME).

High-efficiency anti-tumor nano-drug delivery system containing hydralazine and preparation method thereof

A nanosensor for detecting molecule characteristics includes a membrane having an opening configured to permit a charged carbon nanotube to pass but to block a molecule attached to the carbon nanotube. The opening is filled with an electrolytic solution. An electric field generator is configured to generate an electric field relative to the opening to drive the charged carbon nanotubes through the opening. A sensor circuit is coupled to the electric field generator to sense current changes due to charged carbon nanotubes passing into the opening, and to bias the electric field generator to determine a critical voltage related to a force of separation between the carbon nanotube and the molecule.

Nanospore sensor for detecting molecular interactions

Nanopore sensor for detecting molecular interactions

A nanosensor for detecting molecule characteristics includes a membrane having an opening configured to permit a charged molecule to pass but to block a protein molecule attached to a ligand connecting to the charged molecule, the opening being filled with an electrolytic solution. An electric field generator is configured to generate an electric field relative to the opening to drive the charged molecule through the opening. A sensor circuit is coupled to the electric field generator to sense current changes due to charged molecules passing into the opening. The current changes are employed to trigger a bias field increase to cause separation between the ligand and the protein to infer an interaction strength.

Nanopore device for drug-like molecule screening or lead optimization to a targeted protein

A mechanism is provided for ratcheting a double strand molecule. The double strand molecule is driven into a Y-channel of a membrane by a first voltage pulse. The Y-channel includes a stem and branches, and the branches are connected to the stem at a junction. The double strand molecule is slowed at the junction of the Y-channel based on the first voltage pulse being weaker than a force required to break a base pair of the double strand molecule. The double strand molecule is split into a first single strand and a second single strand by driving the double strand molecule into the junction of the Y-channel at a second voltage pulse.

Base-by-base ratcheting of DNA/RNA in a Y-shaped nanochannel

DNA/RNA in a Y-shaped nanochannel

A method for associating data with a target biological sequence includes identifying, in a network, one or more references to data, where the data has a relevance level greater than a predetermined threshold. The method includes associating the one or more references to one or more probe sequences corresponding to a segment of a biological sequence to which the data pertains The one or more probe sequences are ranked based on one or more criteria and the probe sequences are assigned a level of affinity to a segment of the target biological sequence based at least on the ranking of each reference.

Association of data to a biological sequence

A method, information processing system, and computer readable medium, are provided for analyzing a protein folding process. The method includes conducting an incremental pattern discovery process. The incremental pattern discovery process includes judging multidimensional data from a simulation of a protein folding process. The incremental pattern discovery process captures at least one intermediate data point in at least one pattern associated with the protein folding process.

Visual analysis of a protein folding process

Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

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Stormville, NY, United States of America

Ruhong Zhou