Physics based mesh deformation. This is the physics system.

PhysicsDeformer.cs

using System.Collections;
using System.Collections.Generic;
using UnityEngine;

public class PhysicsDeformer : MonoBehaviour {

    public float collisionRadius = 0.1f;
    public DeformableMesh deformableMesh;

	// Use this for initialization
	void Start () {
		
	}
	
	// Update is called once per frame
	void Update () {
		
	}

    void OnCollisionStay(Collision collision)
    {
        foreach (var contact in collision.contacts)
        {
            deformableMesh.AddDepression(contact.point, collisionRadius);
        }
    }
}