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Collisions in Multiple Dimensions: Problem Solving01:06

Collisions in Multiple Dimensions: Problem Solving

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In multiple dimensions, the conservation of momentum applies in each direction independently. Hence, to solve collisions in multiple dimensions, we should write down the momentum conservation in each direction separately. To help understand collisions in multiple dimensions, consider an example.
A small car of mass 1,200 kg traveling east at 60 km/h collides at an intersection with a truck of mass 3,000 kg traveling due north at 40 km/h. The two vehicles are locked together. What is the...
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Collisions in Multiple Dimensions: Introduction01:05

Collisions in Multiple Dimensions: Introduction

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It is far more common for collisions to occur in two dimensions; that is, the initial velocity vectors are neither parallel nor antiparallel to each other. Let's see what complications arise from this. The first idea is that momentum is a vector. Like all vectors, it can be expressed as a sum of perpendicular components (usually, though not always, an x-component and a y-component, and a z-component if necessary). Thus, when the statement of conservation of momentum is written for a...
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Molecular Comparison of Gases, Liquids, and Solids02:26

Molecular Comparison of Gases, Liquids, and Solids

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Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...
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Hybrid Zones02:29

Hybrid Zones

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Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may possess distinct phenotypic or genetic differences that impact their survival and reproductive success. The genetic variances introduced by hybridization influence species diversity and speciation processes within the hybrid zone.
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Elastic Collisions: Case Study01:15

Elastic Collisions: Case Study

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Elastic collision of a system demands conservation of both momentum and kinetic energy. To solve problems involving one-dimensional elastic collisions between two objects, the equations for conservation of momentum and conservation of internal kinetic energy can be used. For the two objects, the sum of momentum before the collision equals the total momentum after the collision. An elastic collision conserves internal kinetic energy, and so the sum of kinetic energies before the collision equals...
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Related Experiment Video

Updated: Jul 29, 2025

A Visual Guide to Sorting Electrophysiological Recordings Using 'SpikeSorter'
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Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search.

Stephanie Wills1,2, Ruben Sanchez-Garcia1,2, Tim Dudgeon3

  • 1Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom.

Journal of Chemical Information and Modeling
|May 25, 2023
PubMed
Summary

The Fragment Network database efficiently identifies novel fragment merges for drug discovery, surpassing traditional methods in finding potent compounds by exploring vast chemical spaces.

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Area of Science:

  • Medicinal Chemistry
  • Computational Chemistry
  • Drug Discovery

Background:

  • Fragment merging is a key strategy for developing potent drug candidates by combining structural motifs of overlapping fragments.
  • Identifying suitable fragment merges from commercial databases is challenging but crucial for efficient drug development.
  • Synthetic accessibility is a major hurdle in fragment-based drug discovery.

Purpose of the Study:

  • To demonstrate the effectiveness of the Fragment Network, a graph database, in identifying fragment merges.
  • To compare the Fragment Network approach with traditional fingerprint-based similarity searches for finding fragment merges.
  • To showcase the Fragment Network's capability in discovering potent drug candidates.

Main Methods:

  • Utilized a Fragment Network database containing over 120 million compounds to identify fragment merges.
  • Applied the Fragment Network to four crystallographic screening campaigns.
  • Compared results with a traditional fingerprint-based similarity search.

Main Results:

  • The Fragment Network identified complementary sets of fragment merges compared to similarity searches.
  • Both methods successfully recapitulated fragment-protein interactions but explored different chemical spaces.
  • Retrospective analyses identified potential inhibitors with micromolar IC50 values for COVID Moonshot and Mycobacterium tuberculosis EthR.

Conclusions:

  • The Fragment Network is a powerful tool for exploring chemical space and identifying fragment merges.
  • This graph database approach enhances the yield of fragment merges beyond classical catalogue searches.
  • The Fragment Network facilitates the progression of fragments to on-scale potency, aiding drug discovery efforts.